if you could share a file that might help,. ( doesn't have to be a full file., just an example file of a scene that doesn't work )
I tried all sorts of things to mess up the naming ,, and they all work as expected.
A lot of peoples scripts mess up because of naming within a hierarchy.
so if you have
mouth_grp | mouth_offset | mouth_ctl
And when you rename it uses a long name. that can sometimes mess up as the parent gets renamed first. .and then the following children no longer. but that should throw an error.
another issue is clashing node names.. often renaming scripts will mess up on that as they aren't using long names correctly in the script.
but that too should throw an error .
( maya does not like clashing node names. ( as most operations are based on name).. when duplicating I always recommend turning on the "rename children" option.
but I'm not getting that from modify | Search replace names either.
(nor from cometRename )
and sorry, but to double check , this is maya 2025.3 ( and not 2025.2 )
hth
-=s