Hi
I have only just started dabbling in InfoPath 2007 myself but would guess that publishing the template should remove the history. The only thing left then would be the errors. I have just created and tried out your issue and cannot recreate the problem, the logic inspector deletes the rules and all other validation and calculation as soon as I delete them from the form. My only other theory is that there might be two templates with the changes on one but not on the other.
I would like it if you could test out a new blank form create a repeating table and add in a secondary data source. make the first control a DD-Box and fire a rule off it to set the next fields value. Then make the thrid text field's default value relevant to the DD-List. Logic Check them and then delete them and I would not be at all surprised if they are removed from the logic checker the next time you look.
I believe it can only be due to confusion in the templates or maybe if the form is fully trust, thus when you use it and haven't re-installed it it woudl not be updated. I am sorry I can only guess but it is a farily unusual state of affairs.
I hope this helps
Adam