Well, I know of one customer who was allowed to keep his 128k board, as shown in my 512k Upgrade Kit photo. This photo shows the actual box the 512k upgrade shipped in, and the motherboard shown is the 128k board that was removed. When I purchased my pristine Mac 512k machine, it shipped with the original Picasso box, floppies, mouse, keyboard, carrying case, and yes, this upgrade kit with the stock 128k board inside! (I purchased it on EBAY for $400. It also came with some old books, including one on Excel. It came with an original boxed copy of Multiplan, original boxed copy of OverVUE, 4 complete versions of CopyIIMac, 4 boxes of blank Apple branded 400k floppies (most unused without even the labels applied), and other software I can't remember off the top of my head without going downstairs and taking a look. This setup even came with many original receipts for the Mac, upgrades and software. But alas, no documentation on the Mac 512k upgrade.
All of this stuff was used and held by the original owner until he passed on (which is why it went up for auction). As such, I can say for a certainty the 128k board was not bought at an auction later and then added inside that Mac 512k box. I was told that these items had been in storage for a long time. And I can see that too because the machine lacks any yellowing and even the spacebar on the keyboard is in pristine condition and not discolored, like most every spacebar you'll find on EBAY now days.
So I will assume that the original owner simply paid more to retain his 128k board. Since he retained receipts from most everything he every bought in this setup, he seems like the kind of fellow that would do that. And I would therefore logically deduce that Apple would have allowed it, if the customer paid to retain the original board.