Sounds like the LBS is definitely a bit confused. 29er and 700c are the same diameter/circumference. The only difference that will impact what tires will fit what rim is the WIDTH of the tire and WIDTH of the rim. Many road bikes have narrow rims, somewhat limiting the max width of a tire you can put on them. Similarly most 29er rims are much wider, limiting how narrow of a tire you can put on. So maybe you can't (or shouldn't) put a 23 or 28mm tire on a "29er" rim due to width of the rim, Almost any 29er rim I have seen could easily handle a 47mm, and likely a 35mm tire.
There are charts that explain what width tire can go on what width rim online...maybe you should print it out and give it to the LBS?
Last edited by mstraus; 07-28-14 at 11:20 AM.
Reason: fix typo