filemaker pro 11 is not supported on OSX 10.12. It is also past it's complete end of life support.
Sounds like you might have cloned an interface file for a solution designed to use data separation. Since the data isn't in the interface file to begin with, A clone of the interface file is identical to the original and still shows data from the data file. Deleting the records would then delete the records from the data file and both copies of the interface file, the original and your clone will show that the records have been deleted.
Open Manage | Database | Relationships and look at the names of your Table Occurrence boxes and hover a mouse over the arrow in the left corner of each. I suspect that the titles are all italicized--indicating an external data source and that hovering over the corner will show you the name of your data file. You can also see the name of this file in Manage | External Data Sources if I am correct.