Do you have a working Database?
How many tables, fields?
If possible, attach a copy of the FMP file.
First make sure you have a found set of only the blank records. Delete all records in the found set. You should be left with only this records which were not part of that found set.
It sounds like there's a relationship in the database that has "delete related records" (referential integrity) enforced. Check your Relationships Graph and see if any relationships exist between the context where you're deleting and the table where the records are disappearing.
I have found that when the Print Area (in Excel) exceeds the rows with actual data, that's when I see extra columns and rows during import from Excel into FileMaker.
While you may not be able to adjust the print area prior to import, it may be a factor to consider.
Hi Thanks for all the comments, I think it was a bit of everything, I had the relationship set up incorrectly and the print area in the the excel sheet. I think the main issue was the relationships.