To my understanding, the only modification to your file(s) is during the initial upload process where all overlapping shells are merged into single objects. From there, the file is not modified in any way. It's highly likely that something broke after printing, and they were trying to make it good.
From the day that the handling fees were implemented, I've been worried that someday we'd be told that you can have only only on shell per file. Fortunately, they have yet to impose such a rule.
In case you weren't aware.. there was a item added a few months ago to the Edit Model/Details page that counts the number of PARTS in your file. A PART is defined as a shell that can not separated from other shells.. either the shells in your file overlap such that they became a single shell, or they interlock such that they won't fall apart by themselves.
It sounds like your file would contain 30 PARTS. Even though Shapeways is still allowing this at this time, I continue to suspect that it will become a problem for designers when/if they disallow such collections. At worst, we were previously warned.. don't abuse the Part Count.
Thinking of the poor production person, imagine trying to fetch a set of these
http://shpws.me/oCRi out of the printer - only 4mm tall - no sprue - no cage. And remember.. they first clean the tray with an airhose!
The best solution is to sprue or cage your models together such that they can be picked up by a human hand as a single PART - that will remove the chances that they mix two similiar items from two different designers or foul up the part count as happened to you this time.
Take a look at this model:
http://shpws.me/puwG - very small stuff, but even if an item inside the cage were to go diagonal, it still couldn't get out of the cage.