Does a negative commandment linked to a positive one erase the prohibition?
If a person stole and then returned it, is that permitted?
And regarding tefillin, that’s a commandment one simply doesn’t perform, not that one violates something specific (an optional/contingent commandment).
And likewise, let’s assume tefillin on Chol HaMoed also joins the question — that still isn’t really an answer.

A negative commandment linked to a positive one repairs the violation (see the Talmudic passage in Makkot about “whether he nullified it or did not nullify it”). Of course, ideally one does not say, “I will sin and then repent,” but when there is some reason to do so, there is room for the reasoning that it is permitted, or that custom permits it.
Tefillin is not an optional commandment but an obligatory one. Where did you get the idea that it’s merely optional?

Isn’t tefillin not an obligatory commandment every single day?
From the wording of Scripture it sounds like it applies every moment, but the Sages enacted, because of cleanliness, that one should put them on only in the morning. So then there is no nullification of a commandment by not putting on tefillin on Chol HaMoed.
And is it really permitted for me today to begin practicing a custom and thereby nullify commandments?
If I am stringent not to open the refrigerator on the Sabbath even in a permitted way, can I then not eat matzah because of that?

Tefillin is an obligatory commandment. True, the source for the requirement to put them on every day is not clear, but whether the Sages established that or whether that is the custom, that is still the definition of the commandment. In any case, someone who does not put them on one of the days has at least nullified the enactment, and plainly also the Torah commandment — certainly according to Tosafot on Sukkah 4a, that one who does not fulfill the rabbinic requirement has not fulfilled the Torah-level one either.
You may not adopt a new custom at the expense of a commandment. A custom is always something that begins informally, and only once it becomes established is there an obligation to act in accordance with it.
As for the refrigerator, that is not a question of custom but of law. If in your view it is forbidden as a matter of law, then indeed you may not eat the matzah. Obviously.
It seems to me we’ve exhausted the issue.

Which Sages established that one must put on tefillin every day? The Jerusalem Talmud is explicit (almost) that there were amoraim who did not put them on every day.

The Rabbi wrote that we find this, so I ask his forgiveness, but I still didn’t understand: if the matter is forbidden, how was it permissible to begin practicing this way? True, afterward the prohibition was already accepted, but for the first ones wasn’t it forbidden?
And by the way, regarding refrigerators, I meant those who don’t open them even when it is permitted, out of concern that they might accidentally open them when it is forbidden.

Since when is the position of Ba’al Halakhot Gedolot and Rashba regarding refraining from putting on tefillin on Chol HaMoed a mere custom?

Berel the Third and Yankel the Fourth. What do you mean, “which Sages”?
See the Shulchan Arukh and all the halakhic decisors. In the book Yishlach Sharashav, the article of Y. M. Yaavetz was mentioned, dealing with the question of where they learned that tefillin are put on every day. The simple explanation, in my humble opinion, is that it should be constant, but night is not a time for tefillin, and therefore one puts them on every morning. The reason one does not keep them on all day is because of cleanliness.

Some had the custom to put them on and some did not. Both customs appear in the Shulchan Arukh. In the end there are no decisive arguments either way, and seemingly we should have put them on.

The Sefer Mitzvot Gadol, commandment 3, proves the obligation to put on tefillin every day from tractate Menachot against the view of Rabbenu Tam and the Rif:
“Our rabbis further said in tractate Menachot (44a): Anyone who does not put on tefillin transgresses eight positive commandments every day, for there are four passages there, and in each one there is a positive commandment for the arm-tefillin and a positive commandment for the head-tefillin. Our rabbis further said (Berakhot 14b): Anyone who recites Shema without tefillin is as though he bears false testimony against himself. Our rabbis also said in the first chapter of Rosh Hashanah (17a): The sinners of Israel in their bodies, who are judged for twelve months in Gehinnom — this refers to ‘a skull that did not put on tefillin.’ The meaning of ‘skull’ is head, and Rabbenu Yaakov explained this as one who refrained from tefillin out of rebellion and contempt for the commandment, as we say in Yoma (36b), ‘sins’ — these are acts of rebellion. But Rav Alfasi explained (in the first chapter of Rosh Hashanah) that it means one who never put on tefillin in his life. And one may respond to his words that he should have said, ‘who did not put on tefillin,’ and neither of them has conclusive proof that the explanation is as they say. Therefore one must be careful.”
By the way, it seems that if not for the Sefer Mitzvot Gadol, we would not be putting on tefillin every day, because in the time of the medieval authorities they were concerned that the requirement of a clean body meant a body clean of sins. Only the Sefer Mitzvot Gadol innovated that it is possible to put on tefillin at prayer time, and then we are not concerned about a body clean of sins.

Why indeed can a custom nullify a positive commandment like tefillin on Chol HaMoed, assuming that it applies every day?
As I understand it, the reason people practiced this way is only because of Kabbalah, but someone who does not accept Kabbalah cannot base his practice on custom, can he?

Excellent question. I don’t know. Maybe it is like the way the Sages can uproot something through passive non-performance.