I have a very large underground fortress and I've been seeing something unusual with respect to burrows and military alerts. First, I'll describe the normal situation.
I have a giant obsidian farm (40x40 squares, only accessible from within the fort, otherwise blocked on all sides by constructions) which I use primarily to train new miners before sending them off into the field. I have this in a burrow called "Obsidian Farm" and I assign my miner-in-training there (one at a time).
I have areas where I want to keep the stone (gems, ores, etc) in a cavern under my fortress. I have this in a burrow called "Temp Work" and I assign all my already trained miners there.
I have my entire fort encased in a burrow called "Whole Complex" and I assign all my miners (in training or not) to this burrow, since there are no dig designations in that burrow.
There is very little overlap between these burrows, and this system does quite well to allow me to train a miner and use legendary miners simultaneously without having them interfere with each others' jobs.
Then there is a goblin seige.
I set my civilization to the military alert which restricts them to the three burrows mentioned above (Obsidian Farm, Temp Work, and Whole Complex), thus keeping them underground but still able to do their cave-work. Once the seige is dealt with, I look at the Obsidian Farm burrow, and I see several miners working together there. When I set the civilian alert back to no burrow restrictions, the post-training miners stop working in the Obsidian Farm and run back to the Temp Work burrow.
It seems, from this, that military burrow restrictions will invalidate individual burrow assignments. How can I get this to work right?
If it matters, I'm still using 31.03.