The Gemoro on the bottom of 112: in the sugyo of Maaser Sheini tries to find an Ukimto for the din of "Yigonsu", and says that we can't be talking in the case where it was brought to yerusholaim because there is a din of "Koltuhu Mechitzos" and rashi explains that it came to yerusholaim before the city became "ir Hanidachas".
My question is why could the gemoro say that we're talking that the city became "ir Hanidachas" on the way to yerusholaim so until it came to yerusholaim it's still momon govoha and once it got there, there won't be "Koltuhu Mechitzos" but lichora it would still become "momon Hedyot" according to rabonon wouldn't it??? and it would make sense to be gonez it like rashi says in DH: "Ve'im Isa" that even if it's "momon hedyot" it would be nignaz not burned because of "Ziluso"?
As long as the Ma'aser Sheni is b'Gevulin, it cannot become prohibited at all, since it is "Mamon Gavoha." When it is brought to Yerushalayim it should be entirely permitted.
The only reason the Gemara thought that if it was already in Yerushalaim at the time that it will become Asur, is since at the time that the city became an Ir ha'Nidachas the Ma'aser was already "Mamon Hedyot," and therefore it could become Asur. To that we answer "Kaltuhu Mechitzos." However in your case the Ma'aser will not become Asur at all, for after the Gemar Din the Mamon does not become Asur.