Hi Dawn,
Voids should absolutely NOT be necessary. Unapply and re-apply can take some time yes, but it's the only way possible to accomplish what you're describing. Another option would be to not apply the payments until you have the accurate apply information.
I have been working with GP for over 20 years, there has never been a time when you could apply a 'negative' amount to my knowledge. If you have an example of this in your system, perhaps you could post some screenshots? Maybe that will help us better understand what was being done.