Not sure the file you linked in your last post is the correct one.
It's no more a Tower Defense, it is a shooter.
Perhaps you should upload your capx to dropbox
it's easy as managing its own hard drive.
As for your issue, you mention again that all instances of an object disappear when you use an action "Destroy".
I guess it is once again a picking problem.
You don't use conditions such that only the "current" instance gets picked and destroyed.
That's a guess without having seen the code though.
If I follow your logic correctly, once a TOWER is built, its BUILDSPOT is destroyed, so, logically, there should never be a TOWER overlapping a BUILDSPOT.
You can then use a subevent "BUILDSPOT is overlapping TOWER" and an action BUILDSPOT: Destroy
This will destroy any BUILDSPOT that has a TOWER over itself.
Have a close look at the topics listed in the how do I FAQ
at the section "Picking/selecting instance(s)".
The subject is treated in many ways and with different approaches.
Hope it might help you.