My understanding has been that Schubert's 'Gastein Symphony' was presumed lost, until scholars realized it was in fact his 9th symphony (the 'Great'). But Wikipedia tells me the 7th Symphony, D. 729, is a structurally complete work. Is there then a symphony of Schubert's (i.e., of the nine) which doesn't actually exist?
I don't think there is any conclusive evidence that Schubert ever wrote a symphony which is now completely lost.
But considering that he was a very prolific composer who left many works incomplete, and who died young with only about 100 of his 1500 known works actually published during his lifetime, there will probably never be a definitive answer to the question.