If a plugin file is provided by multiple mods then only the first is hidden by mohidden or optional. For example, "OCW_CellSettings.esp" is provided by Obscure's College of Winterhold then overwritten by Ultimate College of Winterhold. When merged the script detects that it's provided by the latter, renames/moves it, but doesn't rename/move the version provided by the former. The script probably needs a "while" loop to handle such situations, but my python-fu isn't up to the task.
If a plugin file is provided by multiple mods then only the first is hidden by mohidden or optional. For example, "OCW_CellSettings.esp" is provided by Obscure's College of Winterhold then overwritten by Ultimate College of Winterhold. When merged the script detects that it's provided by the latter, renames/moves it, but doesn't rename/move the version provided by the former. The script probably needs a "while" loop to handle such situations, but my python-fu isn't up to the task.