If there are still questions about the tank, don't reintroduce fry. By the way, are those fry small enough to be eaten by fish who aren't used to them? (Guess that is a question and a rhetorical question.)

How much air do you have running in your tank? Those are an extraordinary number of bubbles! When you go to change water, is there a way you could skim those bubbles off? If yours was a salt water tank, I would suggest that they are extra protein from fish wastes and or uneaten food. If the bubbles are just staying there, they could block the oxygen/carbon dioxide exchange more than you would like.

Have you changed water recently? While, if you or I are doing partial water changes regularly, 25% is a lot better than 10%. However if the tank has been left along for a couple of weeks with the medicating, maybe a 10% and a 15% change a couple of days later would be easier on the fish. Next week do a 25% change. :)

Do you have a filter with activated carbon in it? Change it. That will help with medicine removal and should also remove some of the substances contributing to the bubbles. In the best of times activated carbon is used up within two weeks. When there is more going on, it may have been used up as a chemical filter before that.

The female fin clamping could be a response to water quality. After a partial water change, look to see if they are still clamping and if they have a whole bunch of tiny, tiny dots on them. That could be the very contageous velvet. It is treatable, if that is what it is, and treatment wouldn't destroy the filter cycle. But boy would I be glad your fry aren't in there.

If they continue scratching or flashing, look to see what is one their sides. If there are critters or worms which are distiguishable, they could be tiny crustaceans or parasitic worms. Those can be treated with an anthelmintic. That sort of med is usually found in an anti-parasite treatment. If they are just treated with the anthelmintic, the nitrogen cycle will not be bothered. If it is a combination with an anti-biotic, yes the nitrogen cycle will again be clobbered.

Look in the Immediate Help section under Camallanus for mention of various anthelmintics and medicines including them.

If the females look better after the first partial water changes but are still flashing a little, they may be responding to the nitrogenous wastes in the water (which are more of a problem until the nitrogen cycle is re-established). A quick fix is to add, maybe .5 to 1 teaspoon of salt per gallon (NOT tablesalt). That will help the fish endure a certain amount of nitrite poisoning and cause the skin to produce a little more protective mucus or skin slime. Don't add more salt with subsequent water changes unless there is still some (but hopefully a reduced level) of itching. If that continues and there are no identifiable "things" on their sides, maybe add 2.5 teaspoonsof salt for every three gallons of water you replace.

Long term, salt is not a part of a guppy's natural environment. Long term, partial water changes are. ;)