Editor version: V1.37
NeoLemmix version: V12.12.0-RC2

I haven't figured out what the cause is yet, but I've experienced several times that all the skills are reset to zero (or sometimes some other number) in a level that I'm editing.

It happens straight after I've opened a level in the editor.

To be clear, are you talking about the skillset, or about pickup skills?

The skillset.

I just experienced the same bug.
I attached the problematic level.

1) Put the attached level to levels forder and play it with Neolemmix 12.12RC.
  : You can see that the level gives you 1shmmier, 1climber, 1swimmer, 1bomber, 1stone,r 1platformer and 1builder.

2) Now close the Neolemmix 12.12RC and open the same level with editor V1.37.
  : All the skills are reset to zero. It's fine if don't save the level though.

3) Open any other level with editor V1.37 and then open the attached level.
  : Now all the skills are changed to the skillset of the level you opened previously.

Thanks, an example level where this happens will be very useful.

Fixed in commit b1a4d07.