You are running PMS on one of the two NASes or on a third computer?
Normally it will give you multiple instances of each media item, as long things like folder and file names are similar (or the same) If you used the right naming conventions it should just work.
Can you give an example of your media naming scheme?
@mshe You could make use of PlexCSV to detect which entry of your library was identified using what agent (MetaDb field).
I did that on my libraries (changed from MovieDB to PlexMovie) and found all old MovieDB items, checked on IMDB for their IMDB ID and did a new identification by IMDB ID of those items only.
If this makes any sense to you depends on the number of “old” items you find
Of course, doing a Plex Dance with your whole library is another option you have.