Try joining an empty server, enter class editor, unlock the module again (it is likely the reason behind not counting kills is that it disabled itself, you can notice it if the module is grayed out), enable it, close class editor and leave server. There should be a message popup that profile data is being updated.
This has worked for me and some people (I had a similiar issue with MK.60 not saving, made everything apart from default guns and modules reset after each game).
It will not bring the kills back, but it might actually allow you to progress.
Also, if you at some point notice that the kills are gone, try to logout and login right away. There's a slim chance it'll help.
The modules aren't un equipping, this is not that issue or I would have said it was. That fix you are refering to is when a skill re locks itself. I never once mentioned that. This is NOt that issue and thankfully the crytek person seemed to know that.
This is when your skill resets to lvl 1 from whatever lvl it was at, in my case level 3. In addition to not accepting new kills.
If you have read my forum posts I was one of those who mentioned the fix to the problem you are refering to
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Please read the post before posting, thx.