What is the version of xEdit you are using?
SSEEdit 4.0.3h (Hotfix 1) (74B3720F)

Describe the bug
When "Clean Masters" removes all masters (due to it being a archive loader plugin or only having things like new keywords), xEdit re-adds Skyrim.esm as a master.

To reproduce
Steps to reproduce the behavior:

1. Copy some Keyword records from Skyrim.esm as New Records into a new plugin
2. Save the plugin, then use "Add Masters" to add Skyrim.esm as a master and save.
3. Relaunch xEdit, then run Clean Masters.
4. Save and relaunch xEdit.
5. The Messages tab will show Skyrim.esm being added as a master, and the new records will now show as overrides or injected records for Skyrim.esm.

Also included test plugin. Using it, you would start at step 3

CleanMastersTest.zip

Expected behavior
xEdit leaves the plugin with no masters, or failing that, properly adds the master in a way that updates internal formIDs.

Screenshots

Additional context
Confirmed that the same issue happens with Fallout 4 if the plugin is set to have a File version of <1.0. Have not tested with other games, but is likely the same.

When the File version is 1.0, Fallout4.esm is not removed because 00000000 (File Header) is treated as a reference to Fallout4.esm (and shows as a could not be resolved error if the plugin has no masters).