For one thing we have the Tosphot in Tractate Yevamot 16a.To Tosphot you have either full holiness or nothing. There is no "in between" state.
The first answer of Tosphot is OK as far as I can see but how can we explain the second answer?
The basic Gemara there says that Amon and Moav are obligated in the tithe for the poor. Later on that same page the Gemara explains the reason being: הרבה כרכים כיבשו עולי מצרים והניחום עולי בבל כדי שיסמכו עליהם עניים בשביעית. "Many cities were conquered by the Jews that came up from Egypt but were left by the Jews that came up from Babylonia in order that the poor will be able to depend on them in the seventh year."
Tosphot asks from, "There are three lands concerning ביעור." One of those lands in עבר הירדן. So the land beyond the Jordan River is obligated in the seventh year laws. The first answer of Tosphot seems OK. There was an area of Sichon and Og that was originally of Sichon and Og [lets call it Area I] and there was an area that these two kings had conquered from Amon and Moav. Area II. Tosphot suggests that Area I was settled by Jews returning from Babylonia, --not area II. The next answer of Tosphot is the one I can't understand right now. There Tosphot says the area that is obligated in tithes to the poor in the seventh year was not even part of the area settled by Jews coming out of Egypt. Or at least that is how I understand Tosphot. But if that is so then how does it fit with the Gemara?
This is only the tip of the iceberg. There are many more questions. For example the Rambam in the beginning of the laws of Truma seems to make no sense. In one Halacha he says everything on the right from Aco until Kaziv is outside of Israel. and then in the next halacha he seems to contradict this. And in the end of that chapter he says the whole area even of עולי בבל is obligated in tithes only by rabbinical decree. But this last question I might have a kind of half way decent answer for. Maybe--I am suggesting- the Jews returning from Babylonia sanctified the land but the sanctification does not set in until all the Jewish people return to Israel.