Been billing podiatry for almost 25 years, and I can say that that Q modifiers do NOT go on DME items such as L2999. So not sure why your doc thinks that putting a Q9 modifier would work on DME item. All Q modifiers are only for RFC claims, if indicated by dx. So onto your issue...
First, L2999 is an unlisted DME code for a lower extremity orthoses. I haven't billed that code ever, since all LE orthoses come with an appropriate L code that describes what is being dispensed. The supplier of the DME can tell you what specific code to bill, and it is often listed directly on the packaging of the DME item being dispensed.
Second, DME items need two modifiers when it comes to podiatry. The first is the KX modifier, which indicates the DME item being dispensed meets the qualifications for that particular piece of DME, and that it has been documented in the treatment note as being medically necessary. The second modifier needed is which side the DME is being dispensed to, LT or RT. So if you dispensed a L1930, the claim line would look like this:
L1930 KX LT
That says the L1930 meets the requirements for medical necessity, and is for the left limb/foot.
Hope this helps!