I did a test of this with the latest PowerStore v2 files and what I experienced was that when I altered the menu the parameters for the specific category links remained in tact, here is what it looks like for me in the code after I finish:
<li><a href="<?php echo($assumedRoot); ?>Products_Results.php?Search=true&CategoryID=<?php echo $row_menuwriter_productcategories["CategoryID"]; ?>"><?php echo $row_menuwriter_productcategories["CategoryName"]; ?></a></li>
I did notice however that the local and remote roots went to their default values, this part I had to update manually after the fact. I also noticed that the split function remained intact for me.
Please describe the exact steps you took when making the edits and I will do some more checking to try and determine what is going on.