As you noted, when you delete a record in filePro, the record still exists as a blank, deleted record. These records will be reused by filePro as you add records in the file.
If you want to remove all of the deleted records from a file, there are utilities available.
There is a free program from Robert Repko called "squeeze" which is available at the bottom of
http://www.hvcomputer.com/download/public.html. However, the comment says it's from 1995, so I don't know if it works with filePro 5.0. (Though I see no reason why it wouldn't, as the format of the map and key files haven't changed.)
There is a commercial program available from Jean-Pierre Radley called "fpkd", which I believe is available on
http://www.jpr.com.
There may be other similar utilities avaiable, but these are the two that I know of.
Note that these programs cause the record numbers of the records to change. Some people have coded their databases to use the record number as a key value of some sort. If this is the case with this database, you need to make sure that changing the record numbers won't affect the database.