There is an MSB tag (Most Significant Byte) which identifies the high order byte of the memory addresses used when accessing the link database. I would expect it to be MSB=1F for a 2413 PLM. Link record 1 is located as 1FF8, link record 2 at 1FF0, link record 3 at 1FE8, and so on. There is a flag byte at the beginning of each 8 byte link record that indicates Controller/Responder type link record, and whether the link record is “active”. You can also watch the Insteon Traffic tab. Look for a cmd1 of 0x28 Set MSB command. The cmd2 value is the high order memory address which I would expect to be 0x1F for a 2413 PLM link record 1.
The only way to clean up the link database is one record at a time if using the SHN Utility. Since you have records for devices not defined to Indigo perhaps that product has a means of rebuilding the PLM link database with only valid devices. I am not familiar with that aspect of Indigo. Also if Indigo has a means of backing up the PLM link database that would be an good thing to do. Very easy for a finger check to create havoc with the results. The advantage using Indigo is that the activity would be done through the PLM serial interface which is much faster. An entire 8 byte link record is moved across the serial interface where doing it over the powerline through the SHN Utility it is done 1 byte at a time.
Yes, you can delete a link record which flags that specific link record as not active. That link record number can then be reused. For example, if you delete link record 1 and do another Display the first displayed link record number would be 2 as link record 1 is no longer active.
It does appear that link rec 55 is the last active link record. I would display the link database starting at link record 54 to be sure it does end there. Pulling the link database over the powerline requires a significant number of Insteon commands. I have seen powerline problems produce invalid data stopping the display prematurely.
The process would be to delete a link record for a device no longer being used. Then use that same link record number to update the link record with one of the EZX10RF Groups.