I no longer use Fences, however, I did upgrade, it warned me that he program will need reinstalling and when I did the upgrade and reinstalled it, it did keep all the settings and so on.
This was with Fances 2.1 and so I think that if anything it will be even more compatible and so I would say that it should be just fine.
So you upgraded with Fences installed/running... and apart from havnig to re-install it, all was OK?
Ta!

