..and you're leveling a subcraft to 60, you're at 59.9 and you get a .2 skillup to cap, will you lose .1 from your 100 craft? This was avoided in retail because post lv50 you could only get .1 skillups.

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No, your 100 remains 100, and I think that the 60 just becomes 60.

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Unless you did the guild test to raise your rank to craftsman youd be capped at 60 anyway?

Forgive the necro bump but in case the OP or someone else may still find this info useful:

If you stay at Journeyman rank on your subcraft, it will be capped at 60 and it won't be possible for you to skill up past 60, thus your lv100 main craft is safe. If between lv58-60 you turn in the required guild test item and promote from Journeyman to Craftsman in your subcraft it is possible to skill up past 60, and if you do skill up even to 60.1 your main craft will drop back down to 99. Ouch. Stupidly, I did this very thing in retail when I had 100 Leathercraft and skilled up just a little too high in Clothcraft. If you have become Craftsman in your subcraft and you don't want to risk deleveling your 100 main craft, the good news is that you can ask the guild to reduce your Craftsman rank back down to Journeyman to keep your main craft safe. I forget which NPC will do it in the guilds (maybe the Guild Master in your particular guild?), but it can be done.

Long story short, leave your subcrafts at Journeyman rank to keep your main craft level safe.