The mentioned plugin(s) needs to be cleaned. Pay attention to similar LOOT messages.
See xEdit Cleaning and Error Checking. The Batch Plugin Cleaner for Mod Organizer or the xEdit Cleaning Extension for Vortex help to automate some of that. Ignore misinformation that cleaning any plugins is not needed or causes problems.
If a master record is deleted (or permanently disabled via the enable parent opposite to player) and it is not referenced by any other record, it can most likely be removed from the plugin entirely.
Deleted references can cause CTD if they are referenced by other records or otherwise used indirectly.