The order of hafrashas trumos and maasros is truma gedola, maaser rishon and then maaser sheni. If one doesn't go in order he trangresses the איסור of מלאתך ודמעך לא תאחר. Rebbe Akiva Eiger and the Minchas Chinuch both say that if one did the איסור, he should fix it by uprooting [שאלה] the hafrasha.
However, if after the hafrasha he ate the remaining fruits it would seem clear that he shouldn't do שאלה on the hafrasha because he would indeed benefit by not transgressing מלאתך ודמעך לא תאחר but on the other hand it turns out that he ate tevel [tevel is מיתה בידי שמים while מלאתך ודמעך לא תאחר is merely a לאו]. So it would seem that he shouldn't do שאלה.
Now we present a big chakirah: A person was mafrish out of order but he did not eat a whole shiur at once but numerous half shiurim. Should he do שאלה in order to save himself from the איסור of מלאתך ודמעך לא תאחר? On one hand, maybe he shouldn't do שאלה because he will transgress retroactively the eating of a חצי שיעור. On the other hand maybe he should do שאלה because it will save him from the איסור גמור of לא תאחר. It is preferable to trangress an איסור of חצי שיעור than a complete איסור.
But maybe one can argue, that since the שאלה is a new action done in order to fix the איסור, there is no היתר, or at least there is no obligation, to fix it by creating another עבירה [in our case אכילת טבל]. But it seems more likely that he should do שאלה in order to minimize the איסור from a complete לאו to a לאו של חצי שיעור .
Now, let us go deeper. Let's say that he should do hafrasha in order to minimize the איסור from a complete איסור to a חצי איסור. The Shulchan Aruch [328/14] says that a dangerously ill person who must eat meat and has two options, either to eat a neveilah or to shecht an animal on shabbos - we shecht for him on order that that shouldn't have to eat a neveilah. Explains the Ran, that qualitatively the sin of eating a neveilah is less stringent than chilul shabbos, but ultimately eating the neveilah is worse because every כזית is a new לאו, so quantitatively it is more stringent than chillul shabbos and we follow the quantitative עבירה over and above the qualitative עבירה.
ZUGGGTTTTT the Magen Avraham, this psak of the Ran is not only in an instance where a person would have to eat numerous חצאי זיתים but even if he has to eat one חצי זית, since there are numerous חצאי שיעור in this חצי זית and yet again we have a problem of the quantitative increase of the איסור.
It would emerge then that according to the Magen Avraham, in our question one should not do שאלה on the truma [unlike we said earlier], because if he does it will turn out retroactively that he ate numerous חצאי שיעור טבל and that is more severe than transgressing one איסור גמור. [We must note that the Imrei Bina argues with the Magen Avraham and says that the Ran was only talking about where a person will have to eat numerous complete שיעורים of איסור].
[Based on the Super-Geshmack sefer בני ראם סימן י by HaGaon HaGadol Rav Avraham Genechovski Shlita . See there for his conclusion halacha limyse].