1. It is common for a Baal Tseuvah to discover that he or she is not really Jewish, or for a potential Ger/Giyoret to discover that they are really Jewish. No big deal (conversion is very “easy” in the case of a Shomer Mitsvos who discovers that he/she isn’t really Jewish). Remember intermarriage has been wide-spread for the last eight generations.
2. If one holds “Reform” marriages, or even non-marital relationships, are in fact valid halachic marriage, one would probably have to assume that all non-frum Jews are at least safek mamzerim. This is a minority position, and probably most non-orthodox marriages are considered void since neither party intended to be married “k’das Moshe ve’Yisrael”. Also there is the rule that a two safeks (doubts, safek goy, safek mamzer) is resolved by going with the least problematic result (cf. issues with Ethiopian Jews).