I figured out a work around. I forgot that when you setup the source, you specific a uniqueness field. It appears that limits the import from reimporting those records no matter what is in the table or what the auto-dedupe rules are for the table.
My solution was to setup a new source using the same report, but without any uniqueness field specified. The result was that the records I wanted to have imported (and had previously deleted) came in without an issue.
The bad news is that the import source still pulled in 2K rows which the table auto deduped 1998 of them. The daily run will likely continue to pull in 2K rows every time it runs which seems like a waste of processing and api calls.