Your questions are kind of confusing but I will attempt to answer some of them.
Before you copy the database from the iPad be sure the database is closed. If you copy while open this will cause issues.
"If I then make any changes and update the database on the iPad, the entries are deleted from both versions."
This is the part I don't understand? How are you doing the import/export or are you only updating one copy at a time?
You can in FM pro Adv share your database for up to 5 users. Simply point your iPad to FM Pro Computer.
As far as your deleted data and other related tables getting deleted this might have to do with because you did not close the database before copying.
Thank you. I'm sorry the question was phrased poorly. I was not closing the document properly on the iPad. It is fixed now.