I ride a REAL Schwinn!
Join Date: May 2002
Location: NH, USA
Bikes: Lemond Nevada City (stock), '00 Schwinn Moab 3 (very upgraded)
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I don't think you permanently damaged it from riding it like that. If you had, the LBS should have told you when you got it back. How noticable is the wobble? Is it enough to rub the brake pads or interfere with brake setup at all? If it doesn't bother these things, than I wouldn't worry about it for now. However, the shop should have been able to get the rim trued well if the rim wasn't damaged.
Are you noticing the wobble when looking down on the wheel from above with a tire mounted? The tire being mounted incorrectly or deformations in the tire such as bulges, etc. could result in the wheel appearing to have a wobble, while the rim is perfectly true.
Edit: Just read Rotifer's post-that could be an option too.