Invisalign seems to have exacerbated my gum disease, what should I do?

A healthy stable mouth yields the most predictable results.  But, some newer tooth movement accentuates/accelerators produce focused inflammation in the bone around the teeth we want to move...allowing the teeth to move more freely.  Periodontal disease is an autoimmune disease which is passed along genetically.  It has triggers and something that is irritating will most likely trigger.  We do use Invisalign like "trays" to protect teeth from damage and to also deliver medicaments to help teeth and gums.  Without wearing retainers, your teeth will "relapse" back to where they came most likely.  This can happen really fast.Get with your treating dentist and find a comfortable and effective solution, ASAP!

I can't speak exactly to your case, but in general, tooth movement during an active gum infection causes the damage to be worse.  If you or your dentist can not maintain you mouth in an infection free state, you should be referred to a specialist.  That is the standard of care here in the states.