I wasn't able to reproduce this, and it had me scratching my head. But I think I have figured it out.
Insurance! If you are insuring something before the raid, it defaults to taking from your character before your stash. This is not the same behaviour as live, and as such is likely a bug. I will bring this to the attention of the devs.
I will mention again that the money found in raid from safes/etc. and put in the safe container also get deleted after death/extraction. I've tried all possible cases, the result is still the same, but only with roubles, euros and dollars work just fine. Also if you put them anywhere else on your person, you can bring the roubles into the raid/extract with them, so that might be something to go on.
