KamSolastor
commented
5 months ago Update: After further investigation, it looks like the new plugin that zMerge was making was being given a 0.95 header version, which meant that it could not properly use the reserved space of 000001 to 0008000 that was allowed with the 1.0 headers.
Opening and saving the merged plugin in the Creation Kit acted as a workaround, resulting in the formIDs properly using the additional space and not overwriting the records from Fallout4.esm incorrectly.
Not sure what would need to be updated in zMerge to let the newly created plugins have a header version of 1.0, but in the meantime saving in the CK appears to work as a proper workaround.
For reference, same plugin and record from the original screenshot after saving in the CK:
When merging, at some point formIDs being renumbered seem to roll over to start at 0000001 and then go up from there, resulting in what should be a door being referenced as a constructible item, such as the example below. The column for the Fallout4.esm entry shows that it should be a door record, yet the record on the left selected shows it is actually a constructible object.