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I haven't worked with the file you refer to, but you are experiencing what is called "cascading deletes".
Go in an check the relationship among all of the tables to be sure that the checkbox to delete all records in table X when deleting a record in table Y is only checked on one one of the two tables, not both. Then check that you don't have it set in other TOs for the same table to trigger deletes where their not expected.
I've know people to set everythig to delete thinking it would clean itself up, only to lose EVERYTHING in all tables when they deleted a record somewhere.
It's all controlled from the relationship graph dialogs for setting the related fields between each pair of related records.
Check them all if you aren't sure where it's coming from, but it's most likely the parent TO of the layout and child TO of that specific portal.
Also, NEVER turn on a related delete in a relationship between TOs for a self-related join.
Thank you for that answer.
As you correctly deduced I had my permissions for creating and deleting files in related record a littl tied in a knot.