While trying to reproduce the issue I think I have stumbled onto the main cause of these problems.
I could reproduce the issue if I double click selected a rule ID then pasted it into CMC disable rule field.
Windows was selecting a trailing space which was then being pasted into the ID field (unseen by tired eyes).
On clicking the save button Apache restarts, but no SecRuleRemoveById line is written to modsec2.whitelist.conf or the other locations it should be written to.
It effectively fails silently.
This could be eliminated with sanitization (stripping white-space) on save action or error message to avoid silent failure.
This is more of a feature request than a bug report, but I thought I'd let you know.