I'm fully aware that is false positive but it is even Windows Defender started to consider it a malware. So it is real QA problem and it need to be fixed.
If you using pyexe you need to recompile bootstrappers. Don't use py2exe ready binaries/wheels - compile it from source in your build environment.
Then check your application exe with
https://www.virustotal.com/
If that not help - replace pyexe with pyinstaller.
EDIT:
My bad - you apparently using pyinstaller already.