So to clarify, if we do this:

Anything done online since w switched up to this point is gone and must be re-entered? (Again 5 admins working daily in here)

And basically we are starting fresh so to speak and importing a condensed file that tricks the online version into believing there are no invoices with sales tax because they are no longer read as invoices, only data?

I'm skeptical to do this since we have had so many problems with the functionality of a program that was supposed to be "better". I can only imagine the can of worms we will open doing something that cannot be undone. 

So again, can't you just override the tax issue in the online programming like it was in desktop? That would easily solve our issue, and is what all the comments previous to mine in this thread are asking for, not tedious work arounds that can't be undone.