I initially was successful in synchronizing notebooks between the desktop and mobile app using my OneDrive as the sync server. The issue I have run into is both applications create a file folder Apps and Apps(1) and they don't link up. Any suggestions on how to get them to communicate to the same folder would be appreciated.
This is entirely a matter of OneDrive than Joplin. I've noticed that Google will also do the same thing in creating secondary copies of folders with numbers after them, just as you describe OneDrive doing.
You need to fix whatever is causing this, whichever device that is making the Apps(1) folder. Shut off each and every device or at least the Joplin app and then go to the online view of OneDrive and rename the Apps(1) folder to another NAME, then use each one of your devices that are using OneDrive as a drive, (Joplin is not the only one that uses it BTW, other can use it too). If you start Joplin and it recreates the Apps(1) then that's the culprit that is causing it. You have to fix the sync that is running afoul.
Good luck, it can be a real snarled up mess. I've had this happen with other apps as well, although since you are indicating sync is not working and perhaps this is the only app you have that uses that Apps folder, then one of your Joplin instances is causing it. You may have to completely remove it and reinstall setting up the sync once again.