I created a Cloud using Kubernetes plugin. It works with our Rancher server. Also, I can find clouds element in config.xml. It still works fine after I restart Jenkins controller.
However, whenever I upgrade the version of Jenins controller and restart it, the clouds element in config.xml would be gone 
. I lose all the Cloud setting whenever I upgrade Jenkins.
I also did a test that after I upgraded Jenkins and the clouds element was removed, I manually restored the config.xml with the clouds element and then started Jenkins. The clouds elements was removed again 
. The only way is to re-create the Cloud setting via the Jenkins UI. Why would the clouds element be removed after Jenkins upgrade? How to fix it?
Jenkins setup:
Jenkins: 2.539
OS: Windows Server 2019 - 10.0
Java: 25.0.1 - Oracle Corporation (OpenJDK 64-Bit Server VM)
JDK_Parameter_Plugin:1.3
PrioritySorter:905.v35c21f62f980
URLSCM:1.6
ace-editor:1.1
analysis-model-api:13.15.0-928.v63f6dc44cfd2
ansible:588.v2a_a_a_f345e34f
ansicolor:1.0.6
ant:520.vd082ecfb_16a_9
antisamy-markup-formatter:173.v680e3a_b_69ff3
apache-httpcomponents-client-4-api:4.5.14-269.vfa_2321039a_83
apache-httpcomponents-client-5-api:5.5-170.v023de017ccd7
artifactory:4.0.8
asm-api:9.9-185.va_6c6b_3348b_c3
atlassian-bitbucket-server-integration:5.0.0
authentication-tokens:1.144.v5ff4a_5ec5c33
aws-codebuild:0.59
aws-credentials:254.v978a_5e206a_d7
aws-java-sdk:1.12.780-480.v4a_0819121a_9e
aws-java-sdk-api-gateway:1.12.780-480.v4a_0819121a_9e
aws-java-sdk-autoscaling:1.12.780-480.v4a_0819121a_9e
aws-java-sdk-cloudformation:1.12.780-480.v4a_0819121a_9e
aws-java-sdk-cloudfront:1.12.780-480.v4a_0819121a_9e
aws-java-sdk-cloudwatch:1.12.780-480.v4a_0819121a_9e
aws-java-sdk-codebuild:1.12.780-480.v4a_0819121a_9e
aws-java-sdk-codedeploy:1.12.780-480.v4a_0819121a_9e
aws-java-sdk-ec2:1.12.780-480.v4a_0819121a_9e
aws-java-sdk-ecr:1.12.780-480.v4a_0819121a_9e
aws-java-sdk-ecs:1.12.780-480.v4a_0819121a_9e
aws-java-sdk-efs:1.12.780-480.v4a_0819121a_9e
aws-java-sdk-elasticbeanstalk:1.12.780-480.v4a_0819121a_9e
aws-java-sdk-elasticloadbalancingv2:1.12.780-480.v4a_0819121a_9e
aws-java-sdk-iam:1.12.780-480.v4a_0819121a_9e
aws-java-sdk-kinesis:1.12.780-480.v4a_0819121a_9e
aws-java-sdk-lambda:1.12.780-480.v4a_0819121a_9e
aws-java-sdk-logs:1.12.780-480.v4a_0819121a_9e
aws-java-sdk-minimal:1.12.780-480.v4a_0819121a_9e
aws-java-sdk-organizations:1.12.780-480.v4a_0819121a_9e
aws-java-sdk-secretsmanager:1.12.780-480.v4a_0819121a_9e
aws-java-sdk-sns:1.12.780-480.v4a_0819121a_9e
aws-java-sdk-sqs:1.12.780-480.v4a_0819121a_9e
aws-java-sdk-ssm:1.12.780-480.v4a_0819121a_9e
aws-java-sdk2-core:2.33.4-62.vc1a_8df64b_4c9
aws-java-sdk2-ec2:2.33.4-62.vc1a_8df64b_4c9
badge:2.12
basic-branch-build-strategies:275.vde2351b_4a_58b_
bitbucket:282.v85a_7e442f57b_
blueocean:1.27.23
blueocean-autofavorite:1.2.5
blueocean-bitbucket-pipeline:1.27.23
blueocean-commons:1.27.23
blueocean-config:1.27.23
blueocean-core-js:1.27.23
blueocean-dashboard:1.27.23
blueocean-display-url:2.4.4
blueocean-events:1.27.23
blueocean-git-pipeline:1.27.23
blueocean-github-pipeline:1.27.23
blueocean-i18n:1.27.23
blueocean-jira:1.27.23
blueocean-jwt:1.27.23
blueocean-personalization:1.27.23
blueocean-pipeline-api-impl:1.27.23
blueocean-pipeline-editor:1.27.23
blueocean-pipeline-scm-api:1.27.23
blueocean-rest:1.27.23
blueocean-rest-impl:1.27.23
blueocean-web:1.27.23
bootstrap4-api:4.6.0-6
bootstrap5-api:5.3.8-895.v4d0d8e47fea_d
bouncycastle-api:2.30.1.82-277.v70ca_0b_877184
branch-api:2.1259.v45c101731c76
built-on-column:1.5
caffeine-api:3.2.3-194.v31a_b_f7a_b_5a_81
checks-api:373.vfe7645102093
cloud-stats:377.vd8a_6c953e98e
cloudbees-bitbucket-branch-source:937.2.1
cloudbees-folder:6.1073.va_7888eb_dd514
code-coverage-api:4.99.0
codedeploy:1.23
command-launcher:123.v37cfdc92ef67
commons-collections4-api:4.5.0-8.va_d5448ef9011
commons-compress-api:1.28.0-1
commons-lang3-api:3.19.0-104.v12125f33a_255
commons-text-api:1.14.0-194.v804a_dc3a_1b_d8
conditional-buildstep:1.5.0
config-file-provider:1002.v93e06b_792d44
copy-to-agent:1.4.4
copyartifact:770.va_6c69e063442
coverage:2.2977.v0e1c1d11042d
cppcheck:1.26
credentials:1447.v4cb_b_539b_5321
credentials-binding:702.vfe613e537e88
dashboard-view:2.543.vca_9da_3cb_9c60
data-tables-api:2.3.4-1451.vb_0b_5238f9054
display-url-api:2.217.va_6b_de84cc74b_
docker-commons:457.v0f62a_94f11a_3
docker-java-api:3.6.0-129.vf6f5db_c0f589
docker-plugin:1274.vc0203fdf2e74
docker-workflow:634.vedc7242b_eda_7
dtkit-api:3.0.3
durable-task:635.v3733cef34b_5e
dynamicparameter:0.2.0
echarts-api:6.0.0-1165.vd1283a_3e37d4
eddsa-api:0.3.0.1-19.vc432d923e5ee
email-ext:1933.v45cec755423f
emailext-template:233.v1eb_88fc160b_5
emoji-symbols-api:17.0-57.v8d44b_9a_b_d5ea_
envinject:2.926.v69c9b_3896a_96
envinject-api:1.235.va_14c74f8f487
extended-choice-parameter:388.ve7b_d0b_920e10
external-monitor-job:223.vb_fddcf42c9b_3
favorite:2.253.v9b_413168133b_
font-awesome-api:7.1.0-882.v1dfb_771e3278
forensics-api:3.1772.v99ca_3d83b_9fa_
gatling:1.3.0
git:5.8.0
git-client:6.4.0
git-parameter:444.vca_b_84d3703c2
git-server:137.ve0060b_432302
github:1.45.0
github-api:1.330-492.v3941a_032db_2a_
github-branch-source:1917.v9ee8a_39b_3d0d
gradle:2.16.1149.v711b_998b_0532
greenballs:1.15.1
groovy:497.v7b_061a_a_de65d
groovy-postbuild:272.v52a_03efb_8653
gson-api:2.13.2-173.va_a_092315913c
handlebars:3.0.8
handy-uri-templates-2-api:2.1.8-36.v85e4cb_234a_13
htmlpublisher:427
http_request:1.22
instance-identity:203.v15e81a_1b_7a_38
ionicons-api:94.vcc3065403257
ivy:582.v35fb_da_0312f7
jackson2-api:2.20.1-423.v13951f6b_6532
jacoco:3.3.7
jakarta-activation-api:2.1.3-2
jakarta-mail-api:2.1.3-3
jakarta-xml-bind-api:4.0.5-3.v3d5b_a_73965b_9
javadoc:354.vee1a_660b_4990
javax-activation-api:1.2.0-8
javax-mail-api:1.6.2-11
jaxb:2.3.9-133.vb_ec76a_73f706
jdk-tool:83.v417146707a_3d
jenkins-design-language:1.27.23
jenkins-multijob-plugin:662.vd2e0001f6b_b_d
jersey2-api:2.47-165.ve7809a_3e87e0
jira:3.19
jjwt-api:0.11.5-120.v0268cf544b_89
job-dsl:1.93
jobConfigHistory:1356.ve360da_6c523a_
joda-time-api:2.14.0-149.v1c3ce991d1b_9
jquery:1.12.4-3
jquery-detached:1.2.1
jquery3-api:3.7.1-619.vdb_10e002501a_
jsch:0.2.16-95.v3eecb_55fa_b_78
json-api:20250517-173.v596efb_962a_31
json-path-api:2.10.0-202.va_9cc16c1e476
jsoup:1.21.2-66.v6ea_38164b_8a_2
junit:1372.vfea_f21efa_b_26
keyboard-shortcuts-plugin:1.4
kubernetes:4392.v19cea_fdb_5913
kubernetes-client-api:7.3.1-256.v788a_0b_787114
kubernetes-credentials:206.vde31a_b_0f71a_c
ldap:793.v754d6b_41b_ea_4
ldapemail:0.8
lockable-resources:1438.v3c0f8c9e2060
mailer:522.va_995fa_cfb_8b_d
mapdb-api:1.0.9-44.va_1e1310c9118
matrix-auth:3.2.8
matrix-project:870.v9db_fcfc2f45b_
maven-plugin:3.27
mercurial:1323.ve69d2a_db_8a_b_d
metrics:4.2.37-489.vb_6db_69b_ce753
mina-sshd-api-common:2.16.0-167.va_269f38cc024
mina-sshd-api-core:2.16.0-167.va_269f38cc024
momentjs:1.1.1
monitoring:2.5.0
msbuild:1.37
nunit:617.vb_152b_0a_7d168
okhttp-api:4.12.0-195.vc02552c04ffd
oss-symbols-api:424.ved751e062911
pam-auth:1.12
parameterized-scheduler:285.ve611986d4c48
parameterized-trigger:873.v8b_e37dd8418f
pipeline-aws:1.45
pipeline-build-step:571.v08a_fffd4b_0ce
pipeline-graph-analysis:245.v88f03631a_b_21
pipeline-groovy-lib:776.vfee5327b_b_a_5b_
pipeline-input-step:540.v14b_100d754dd
pipeline-milestone-step:138.v78ca_76831a_43
pipeline-model-api:2.2277.v00573e73ddf1
pipeline-model-definition:2.2277.v00573e73ddf1
pipeline-model-extensions:2.2277.v00573e73ddf1
pipeline-rest-api:2.38
pipeline-stage-step:322.vecffa_99f371c
pipeline-stage-tags-metadata:2.2277.v00573e73ddf1
pipeline-stage-view:2.38
plain-credentials:199.v9f8e1f741799
plugin-util-api:6.1192.v30fe6e2837ff
popper-api:1.16.1-3
popper2-api:2.11.6-5
postbuild-task:78.v24529f1f5cdb_
prism-api:1.30.0-630.va_e19d17f83b_0
progress-bar-column-plugin:11.vdef198c2d6c1
promoted-builds:992.va_00888f21b_74
pubsub-light:1.19
run-condition:243.v3c3f94e46a_8b_
scm-api:712.v8846fdd68c88
scm-filter-branch-pr:222.v72301ecb_a_ee7
script-security:1385.v7d2d9ec4d909
scriptler:432.v872ed6cd6d5b_
shelve-project-plugin:3.3196.v0052de37a_8d3
snakeyaml-api:2.5-143.v93b_c004f89de
sonar:2.18
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ssh:158.ve2a_e90fb_7319
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ssh-slaves:3.1085.vc64d040efa_85
ssh-steps:2.0.79.v1d1b_5f76dda_8
sshd:3.374.v19b_d59ce6610
structs:353.v261ea_40a_80fb_
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