Just to clear things up.
Save to disk CAN save to your computer disk. But the (any Calibre) LIBRARY should never be the target.
Copy TO Library (on context menu) is an approved way of moving (or copy) a selection to another Calibre Library on (connected drive) the same system
I have an 'Intake Library' where I import books... Beat the metadata into submission
... Only then, do I Copy to Library 'Main"
I don't trust full AUTO anything. Auto Merge only allows Merging if the format is not duplicate. (My wish list is an
Empty Book in 'Main' ). All other merges are either Manual or a cut and paste (typically comments. The other field values are usually available from the lookup pulldown)
Combining books is NOT automatic. For that, there is EPUBMerge
(and lots of user carefulness)