New recordings are lost after reopening, just empty tracks are left

Solved as follows: Simplify, simplify, simplify. Radically. Please read the precautions below before hacking away in your song!

What I did:

• I went through all comps. Removed every take I'm never gonna use which is 90%. Comps got a lot simpler, mostly 2, 3 or 4 takes.
• Where possible flattened to regions to single takes and removed all others.
• In one case exported a complex comp to new track and deleted the original comp (export it, don't use flatten&merge, it is unreliable on complex comps)
• I had live drums, 11 tracks (edited as group), which had become a patchwork of takes starting at many different places in the song. Times 11. After removing takes that won't ever be used, I cut the entire comp in half at a strategic place (just with the scissors tool) and this made each half a lot simpler again. This may well have been a culprit.
• I ran into sketchy looking vocal tracks comps, multi-mic tracks that were recorded simultaneously but the structure was different, had empty takes and lengths that made no sense. Yucky. Obviously a bug. These may have been a culprit. Cleaned and exported to new track, then used the glue tool, this causes a new single-take file. Removed the original comp altogether.
• After a round of cleanup I did "select unused" + "delete files" in the audio bin to destructively throw them out.

Song project got 12x smaller and starts up much faster.

So far new audio recording goes ok. Regulary quit/reopened to be 100% sure, but so far so good! Phew.

Logic's track/region/comp system is still fragile and full of bugs. Especially if a some parts were recorded separate first and later recorded in 1 go on the same track. Logic does not like that. Complex overlaps makes Logic go messy.

Precautions:

1. Export alternative to new Logic project file first. This will leave out any files that should have been deleted but weren't. So whatever mistake I make I have an original to repeat it. Plus: It cut file size in half! (hey Logic, what is that mess coming from? Undo takes?)
2. Set number of backup versions to 30 in the general preferences. Save often, so you have options. Extra storage is negligible, song files are just a few MB.
3. I did the entire procedure in a few smaller cleanup rounds, so I could remember what I did and review it.
4. In between each round, quit/reopen Logic sometimes to see if song was still intact.
5. Played the song to be sure no tracks had shifted while the wave forms appear normal on screen; another bad habit of Logic. Made sure that just before each "delete files" I had a backup to my time machine.

@Apple: Logic's track/region/comp/take structure is super fragile. Please refactor to more modern, robust data structure. Data damage is very expensive in professional recording. This took me an entire week. This was a problem in 2008 and it still is a problem in 2018.

If permissions were a problem, it would not happen halfway a recording session at a predictable point like I describe. Also I would see error dialogs all over the place when reopening the project. Nonetheless I checked, permissions for succesful and failed recordings are the exact same: r/w for me, read for group and world. Other projects in the same folder function just fine. In case you wonder; it is a package and I have over 300 GB of disk space left.