When I spoke to the Allen Edmonds Recrafting department, they did mention that any natural expansion in the cork area of the shoe would be lost through the recrafting process - because recrafting returns the shoe to the original out-of-the-box fit. They mention they have seen nearly whole size differences over time, and when customers got back their recrafted shoes they complained because the shoes felt like they were too small.
They did, however, mention they would consider a custom note attached to the returned shoes to have them inspected in order to preserve the current "fit" - rather than completely restore the shoe to the original size which may now be too small for the customer.
People get used to their shoes fitting a certain way, and they forget how the felt when they were new, so none of that surprises me.
The returning of the shoe to it's original "out-of-box" fit is acceptable and should be expected to some extent. However, there is variance in how much this takes place from pair to pair. They replace the cork, which theoretically removes some of the impression your foot left in the cork insole, but not entirely, as leather has a "memory". Obviously, your impression will return within a couple of wears.
When a Goodyear-welted shoe is repaired, the welt is typically removed and replaced in addition to the sole. When the welt is removed, this leaves the upper temporarily unsecured to anything. If the shoe is not on it's original last, then when the repairman is stitching on a new welt, it risks not being stitched in the proper place to maintain the original size and shape. This can permanently alter it's size. B. Nelson uses sized lasts when they work on shoes, but they aren't going to be as perfect as the original last from the manufacturer. Since B. Nelson uses lasts, they are certainly better than the average cobbler. However, you are risking your shoes to a certain extent even if they are sent to the original manufacturer for recrafting, so sending them to anyone else increases the risk even more.