There are many areas of halacha where an issur drabonon can potentially impact a doraysa and the question is whether the Torah regards an issur drabonon to be permitted, or as an issur. For example the braisa says that just as one cannot be yotzei matzah with bikurim since it can't be eaten בכל מושבות, one should also not be yotzei with maaser sheini. Rashi explains that since maser sheini, once brought into yerushalayim can not be taken out to be redeemed, there is no heater to eat it בכל מושבותיכם therefore one should not be able to be yotzei their mitzvah of matzah. Rashi points out that the issur to take it back out and redeem it is only drabonon yet it would be a Torah recognized issur and prevent maser sheini from being regarded as something that can be eaten בכל מושבותיכם. Tosafos on 38a d.h. aval says this exact point in their second answer.
Similarly, when the gemara 35b says that one can't be yotzei matzah with tevel that is only tevel drabonon, rashi explains that the problem is מצוה הבאה בעבירה implying that even an issur drabonon will be regarded as an aveira and prevent the mitzvah doraysa from being fulfilled. However, the maharsha points out that an issur drabonon can qualify as an aveira for מצוה הבאה בעבירה but apparently not for the concept of מי שאיסורו משום בל תאכל חמץ לבדו that rashi quotes on the top of 35b from ravina on top of 36a.
A similar idea is found in Tosafos 29a d.h. ein, that an issur drabonon of not being able to redeem kodshim to feed to dogs can cause there not to be an issur doraysa of meila. Tosafos explains דכיון דאמרו רבנן אין פודין לא שויא מידי. However, Rashi 7a needs the concept of hefker beis din to explain why an issur hanaah drabonon would prevent kidushin doraysa. From the fact that rashi doesn't say simply that once the rabbonon don't permit benefit it is essentially worthless, implies that rashi holds an issur hanaah drabonon isn't considered worthless by the Torah.