Probably 10 or 12 years ago I had to do the same thing.  I found that mailing multiple things in one envelope resulted in only the top one being processed and everything else ignored.  I tried applying refunds to the subsequent years and there were mixed results, so I would give it a try.  I did one-time have a return where the individual have moved out of the US and was not a citizen, so would not have had a filing requirement if he didn't have US income.  He got a W-2 in a later year for some stock vesting but never filed a return.  Probably 4 years down the road he received an IRS notice and came to me to resolve.  I assisted him with filing the return and he was due a refund of close to $100k, but told him not to hold his breath.  Even assuming he had an automatic extension for being outside the US, he was too late.  The refund was initially disallowed and I did a little bit of follow-up with the IRS which was also denied, but then a refund appeared out of nowhere.  I always though he should have given me a little extra thank$, but I got just an ataboy out of it.  Point is, it doesn't hurt to try.