I guess the aggravating thing for me is just how much of a perfect woman for Henry Grace is. Part of me wishes Henry would just get over it and realize that she's the one for him, but that's not in Henry's nature. As it stands, short of admitting to her the truth (an idea Henry was dead set against a few episodes ago), I'm not sure what he can do, except grow further from Grace. I almost wonder if Henry is, at least subconsciously, expecting things to go back to normal (which is what I'm expecting the season finale to be about), in which case, he's lose another woman he loved (and putting him in the reverse role with the "old timeline" Grace, where he's the one who was in a relationship and she's the one who has no clue what he's talking about).
As for Warehouse 13, they did say that the further from Eureka something is, the less likely it changed, which says to me that Warehouse 13 existed in the other timeline too, though if things do revert, the Claudia/Fargo relationship could end up like Henry/Grace. On the other hand, except for mentioning he was the head of GD, the whole thing could have happened the same way (which would make sense, since I thought it was a little odd that Fargo was the one to go. In the "old timeline," I couldn't see Allison going, as it would be more likely that she'd send Fargo anyway). The premise almost seemed like it was planned before the "new timeline" stuff in Eureka and a line was added to acknowledge it. So if things revert, I expect "13.1" to remain relatively unchanged, whereas things might have gone different for "Crossover," maybe even to the point where Claudia never came to Eureka.