I see this after an upgrade from 9.8 to 9.9 (and before) ..
I deleted setenv.sh and upgraded. Then before start I edited the new file with my custom settings. (memory and custom CA..)
The "ignore and continue" button does not work.
Upgrade: Custom changes have not been carried over
The listed configuration files contain custom changes. To keep your current configuration, re-apply these custom changes to the new version of the files during upgrade.
Note: Make sure you only copy over the changes not the entire files.
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