Hi, I think I have a possible solution if I understand correctly what you need to do.
What you have to do is: Load the original file that doesnt have the transforms you need to do for the welding, etc. Go to the right side of Zbrush where the modifiers are and go all the way down to the export subtab. Copy somewhere the transforms that you see for all 3 axis. After that, you can open the files that you already worked on and that you applied the transforms you needed and go to the same "export" subtab and paste the transforms you copied before (this file should have different transforms). After copying the transforms, export the file and then if you import it, it should have the original position it had before you did anything to it.
It works for me most of the time.
I hope this helps you...
Leo