After upgrading a 7.8 project to 7.9, using -Drepo.bootstrap=true, the boostrap configurations should have been configured properly with no (or little/ignorable) left-over configurations from 7.8 or missing configurations for 7.9.
However, this turns out not to be the case, yet. For several modules, repository, CMS, channelmanager, (forge) plugins, etc, there is still left-over or missing configurations.
This issue is specific to fixing these things for the repository provided bootstrap configurations.
The typical way to test and verify this is as follows:
a) backup the repository data of your current 7.8 project
b) upgrade your project (code, configuration) to 7.9
c) startup the upgraded project using $ mvn -P cargo.run -Drepo.bootstrap=true
d) open the console application and select a configuration base node for which to validate the upgrade and reload-on-startup was done properly
e) for the selected node, invoke the 'Create Patch' action from the top menu
f) the resulting 'patch file' should not contain any (or at most only trivial, ignorable) INSERT, UPDATE or DELETE actions
Note: you need to read and interpret the patch file in reverse, as it represents the changes needed to keep and recreate the current selected configuration to be applied on a 'clean' (non-upgraded, modified) bootstrapped configuration.
So, finding a DELETE action actually means in this case that the bootstrap configuration contains extra configuration which wasn't (re)loaded..., and an INSERT means you have some extra left-over configuration from 7.8 which hasn't been cleaned up/removed.