I think it is time for you to re-visit how you capture these files. 107mb is absurd. No wonder you are cleaning them.
The majority of good captures are under 500kb. Most conversion programs will not handle that large of a file. So I did it the old fashioned way using hcxpcapngtool. It still does not have the valid handshakes to convert.
Maybe try something basic like wifite2. Easy to install and works great.
https://github.com/kimocoder/wifite2
What program are you using to capture? It is not working. Looks like the cleaning is not corrupting them (even though you should never clean cap files), but the capturing is.
You say these cap files are tested as valid. Perhaps in some way they are, but not for M1, M2, M3, and M4 handshakes.