I recently flooded my neglected DSM tank and I didnt have to crank up the co2. What wasn't already dying from the neglect survived and are growing quite well. I'd say no to cranking up co2 excessively. You could do it for peace of mind though, I think having healthy emersed HC is the most important part. Maybe you should have purchased emersed HC to start with because your HC is probably just adjusting, I've never had a hard time growing HC emersed in any of my tanks and it always grows like a weed taking very little time to adjust.
As for fungus gnats, get a regular water bottle, cut the top right above the label. fill with some fruit vinegar and then add some liquid dish washing soap, mix gently, invert the cut top and put it on the bottom half of the bottle so the spout is facing inwards and then tape the edges together. This trap is super effective for fungus gnats and fruit flies. They're attracted to the sour sweet smell of the fruit vinegar and then they go inside. The soap breaks the surface tension of the vinegar so when they land they sink in and drown. They can't fly back out the spout either, not sure why but this trap applies to catching planaria, shrimps, snails etc.