Life cycles differ depending upon the species of nematode. I posted a link, twice now I believe, to Dr. Yanong`s protocol.
http://edis.ifas.ufl.edu/fa091
As stated in that link -
"Nematodes, or roundworms, have been found in numerous species of fish. Because they are similar to other worm-like parasites of fish, proper diagnosis is important for effective treatment."
If your diagnosis is correct, the larval stage of those nematodes will also be killed, but yes, clearly you want to remove as much dead or "paralyzed" worms as possible after treatment. Same with feces, same with filter media.
My suggestion would be quit trying to overthink this, and just follow the protocol as outlined in the link above. At some point your fishes immune system has to pick up the slack, and its immune system will be the final deciding factor. This is how the vast majority of hobbyists have approached fish with worms, for decades. I treated the fish, and never looked back. No scope, no need. All Systems Normal. You see signs of worm infestation, you treat, and problems go away. If problems keep coming back after treatment, and after possible retreatment, then you have to decide how best to continue.
A common sense approach and following proper documented protocol has
almost always worked for me - with the caveat of this - in todays fish rooms there can be super bugs found, pathogens/parasites that do not always respond to typical medication, or those that are completely immune due to decades of overuse of certain meds within aquaculture circles. We have fish imported from SE Asia, mixing with fish in Florida ponds, mixing with wild fish from all points on the globe, and sometimes things are already beyond our control before these fish even reach the LFS. Not all farms have strict biosecurity measures in place, some probably have little to none. Imagine what happens when a hurricane hits a farm with open ponds and concrete vats. Fish & water, and numerous organisms (good and bad) mixing everywhere.
The good news is, it sounds like your fish got a good cleaning out from the initial treatment, so another treatment in 2-3 weeks should completely resolve the problem. If you want to treat again 2-3 weeks after that, it probably won`t hurt, but I have personally never required a 3rd treatment to eradicate worms.