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Blinking is not a side effect of acyclovir. Should her eyes start with discharge or swelling - take her to her doctor promptly though in case she has an eye infection. I'm sure being in the hospital all this time she's been exhausted and rubbing her eyes and such more in general to boot.
When you say her hsv1 went systemic - what do you really mean? I believe you are using that word in the wrong context. Chances are good that your daughter contracted hsv1 orally which is pretty common in kids and then from having her fingers in her mouth frequently like all babies her age do she spread the virus to her hand area. Starting out with blisters on the thumb and then going down the hand/arm somewhat isn't too unusual at her age especially since this has all happened within a month - it's the virus running its natural course. If the virus was systemic - it would be affecting other body parts besides her oral area/hand area which is why I question your use of that term ( and she'd be a heck of a lot sicker too ).
Secondary bacterial contamination is also fairly common in babies her age. Everything is in her mouth, she's down on the floor and pretty much into everything when she's feeling well. It happens at that age. It's good that they've covered her for that too during this.
Does she seem pretty uncomfortable at this point or not too bad? You can throw some baking soda or a packet of baby aveeno bath into the tubby with her and let her splishy splash in it too to help with itching on her hand/arm and diaper area. Plenty of tylenol too. Is she able to drink well with the cold sores?
Sorry to hear that your daughter has had to go thru all this :( It doesn't happen often but it can happen in children her age due to the immune system not being fully mature yet ( and the way babies naturally are - everything goes in the mouth! ). Hopefully once this first infection has fully run its course within the next several weeks recurrences both orally and on her hand are few and far between :)
grace