YEP -- you are worrying about the same things that I was. In fact, I was terrified: I had backed up the FTM file, but knew that restoring from a back-up involves lots of headaches of its own.
But after talking with a friend who had been through the same thing I did the un-link/reconnect thing over the weekend. Everything seemed to go well, and I've been able to 'synch' subsequently with no problems.
Keep in mind that you are de-linking -- NOT deleting. You disconnect your existing FTM file from ACOM, then go through the steps of creating an entirely new file on FTM by downloading from ACOM. So, in my case I now have Generations and Generations(1) on FTM. The first one is the 'old' file and the second one is the 'new' file that I will use henceforth.
One thing that won't be in the new FTM file is your FTM 'to do' list -- which makes sense because it isn't on ACOM. You can still access the old one. I actually printed it out and am taking the opportunity to do some housecleaning as I manually add it on the the new FTM file.
If you decide to go ahead, be sure to make a back-up file. (Since I'm so paranoid, I do mine on a 'stick' so that I'm sure it is safe!!) It is probably also a good idea to run the compacting routine on FTM -- if only to economize space make sure things run as quickly as possible.
I hope all goes well, and I'm sure it will. The only real problem is that we are still subject to the vagaries of ACOM and the persistent lack of quality support!