When I broke a compact machine to move it it spat out the sludge boiler and ender tank inside into my inventory, and was empty when I re-entered. Also, I didn't get my EnderIO conduits back, and that's tragic. This presents a bit of a problem in that once I place and fill a block I can never move it again without massive hassle and/or risk.

Perhaps the best way to fix this might be simply linking a given block, once first entered, to specific coordinates in the machine room dimension, and leaving whatever is there in the room, to be accessed again once the block is placed again. It seems to me that this would be easier to implement than whatever you have going to return the contents of the machine when it's broken.

You can upgrade a Compact Machine with a Nether Star to make it retain its contents when being broken.
You can configure the maximum amount of items being dropped in the config. (In pre 1.10 versions there was an additional bug when breaking CMs not fully breaking all blocks inside the CM).