Agayle,
A good question that I have myself.
You can save the entire file as a HLM using File > Save-as, or a portion of the PLN using File > External Content > Save selection as module. Be careful when saving using the External Content method as there is a checkbox that, which if selected will group the selection, and you may not want that.
Because I sometimes will save a selection, like an apartment unit or bathroom as a module, I just got in the habit of keeping both the original PLN as well as the MOD files.
Also, I will complete the condocs for each building in their own PLN file, then combine in the master site PLN using the project chooser.
Separately however, for Visual Legends (favorites), I only keep and modify/maintain the MOD file. Those files do not have Layout Sheets in the Layout Book.
So, to answer your question, I keep the PLN files & overwrite the MOD files as the project evolves, however I do see that it appears the MOD file may be able to achieve the same. For 'Legends' HLMs, I only keep the MOD file.
Hope that's not too confusing, and is most of what I know on this subject. Keep us informed on your progress.
AC27 v. 4060 w/ MEP, Cadimage, Twinmotion 2023.2.2 using AC from AC6.0, 2021 MacPro M1 chip, Adobe CC. Used AC on both platforms.