Picking up an Assembling machine 2 with Quality module 1 (Normal) causes the entity to disappear. You receive the contents of the machine but not the machine itself.

Note that when you mine an Assembling machine with quality modules, you get a base assembling machine and the quality modules - not the combined machine. In general you should not use the combined machines other than for working with bots. Use the mark around machines to insert/remove the modules.

Are you sure the machine completely disappeared rather than went into your normal assembling machines?

If so, do you have a save where this happens?

I see now. I was looking for the configured Assembly machine, didn't notice the change in normal assembling machines. Thank you!