Well, you wouldn't want to put vaseline'd clothing in your washer along with a GoreTex parka. That is, if you value the GoreTex. Dunno if it's a general problem with riding shorts though. If you ever do paid rides (metrics, centuries and such), they frequently have freebie saddle cream giveaways in the goodie bags or vendor tables. So keep your eyes peeled.
Preventing friction may keep it from getting worse, but if you're already "sore", you'll need to do more. There are camps that talk about keeping things dry and breathable (loose cotton undies) when not riding. Others push triple-antibiotic ointment on the nether regions. I had sores once and it took months to get rid of 'em. I probably didn't do any treatment consistently, but maybe the sores just ran out of patience before I did...