This particular case is regarding a version change, we were applying the latest service pack to a client for GP 2013. So it would move them to GP 2013 R2. Well, with this came a change in how Mekorma MICR stores the path to the stubs library. In the original versions, paths were specific to a workstation/install. But in GP 2013 R2 and later, the paths are a global setting (which is definitely a good thing).
In this case, the client had two machines- a SQL server and a terminal server. And there was a GP shared location where all of the normal reports and forms dictionaries, amongst other shared resources, were stored. The update was applied to the SQL server first, whose stubs library was pointed to the GP share.
The issue came after we updated the terminal server and found that our modified stubs were missing! Well, as it turns out the terminal server was actually pointed local for the stubs library. So when the global was set to the shared location (where there were stubs, since the SQL server was pointed there previously), the terminal server was no longer viewing the previously modified stubs.
Easy fix fortunately, we located the stubs on the terminal server and copied them over to the share. But an important point to note, especially if you have numerous workstation installs as well. We are careful to check for local reports and forms dictionaries, but we are now going to check for local stubs libraries as well when applicable.