Unlike the Windows version, PERRLA for Word on Mac has to run side-by-side with Microsoft Word. There are all sorts of technical reasons for this, but the simplest is that Apple and Microsoft forced us to move PERRLA out of Word.
That means that using File/Save As in Microsoft Word will break PERRLA's ability to work with that paper.
Since PERRLA for Word runs outside of Windows, it has to keep track of where your paper is saved on your computer.
When you use the File/Save As in a Word document you are really opening a new version of your paper and closing the old one. For instance, if I was working on "Paper 1" and then used File/Save As to create "Paper 1 Altered", Paper 1 would be closed and Paper 1 Altered would be open. Any changes I make are made to Paper 1 Altered and not Paper 1.
When you use File/Save As in Microsoft Word, PERRLA doesn't know that you're really working on a new version of the original paper. PERRLA is still working with the original, closed version of your paper.
The next time you try to make a change with PERRLA for Word after using File/Save As, PERRLA will either show you an error message or it will open the older version of the paper (the version you were using prior to File/Save As).
If you were to keep writing in the new version of the paper, then save and close it. The next time you told PERRLA to open that paper, it would actually open the original paper you had before you used File/Save As. So it would look like the content you wrote after the Save As was lost. It wasn't, it's just saved in the other version. You can still find the newer version in the Finder wherever you saved it.
Use Paper Details to change your paper's filename
This usually happens to students who need to change their paper's filename before submitting it to a professor. So, while your paper may be titled "Sasquatch: The truth revealed", your professor may require you to name the file "Bio 402: Section B Pack, G".
In this case, you can change the paper's filename using the Paper Details tab in PERRLA. Just enter the paper's appropriate filename and click Update. That will keep PERRLA attached to this version of your paper and update the paper's filename.