Thanks for posting the save file. The error message is being printed because there are miners inside the blueprint lab surface, and SE can't tell AD what kind of pipe to use there. When the mod configuration changes, AD re-scans all surfaces for miners without ores under them and tries to deconstruct them. You probably placed a bunch of miners in the Blueprint Lab (without any ores) and Cargo Ships was simply the first thing you updated after that.
I can fix the error in the next release of AutoDeconstruct (it should use normal pipes). Though maybe AutoDeconstruct should ignore blueprint lab surfaces anyways.