Every now and then (don't you love that), either Eeschema or Pcbnew leaks a massive amount of filedescriptors, leading to it using up all available descriptors, and failing to save ones work. Previous save seems to be intact in .bak files, although that has failed once for me.
In typical use, the Kicad processes uses 148 descriptors for me. Seems unchanged no matter what I do.
However, every now and then, it shoots up to 1025 (ulimit on my system), and it fails to save files.
Unfortunately, I haven't been able to track down exactly what causes it. However, as it just happened, this is roughly what I did:
1. Create new 625 pin footprint (simple array)
2. Start creating the schematic symbol for the component.
3. While creating the component, created a dummy schematic to just connect the pins together, so I could get an idea of the floorplanning of the BGA (i.e, connect together all GND pins, all 3.3V pins, etc).
4. About 200 pins into this process, it failed.
(Of course, I save the footprint and "F8" from Eeschema quite often during this process)
KiCad version: 6fdc5972f8431b4d5831a32649e67bfe20d05de8 (I.e, post 5.0)
OS: Linux 4.17.2
I suspect this is what @Hildo was seeing too.