Some plugin (several in fact) such as phpswitcher, opendkim and so on need to either inject their configuration snippet or override default configuration when i-MSCP is updated (eg, when configuration file are regenerated). This is for why we cannot disable them. Generally, I recommend to disable them in errata file when I know that current plugins version will not works with newest i-MSCP version.
Administrators should in order:
- Disable plugins through plugin interface
- Process i-MSCP update
- Re-enable plugins (and update them if needed)
Plugins compatibility check is done by the frontEnd atm. In version 2.0.0, we will improve that but for now, I do now want add extra work on installer side to prevent any new bug.