One of these validates the number of logical components in the LMDB versus the old SMSY.
When I ran this validation check, there was a slight mismatch, more rows were found in the LMDB compared to the SMSY. But no further information was provided.
So, to be able to work out which logical component was missing, I had to manually compare the table content of table SMSY_SYSTEM and table LMDB_LC_HD.
From this I found the logical component that I needed to remove from SMSY and I then removed it using SMSY.