Hi, is it permissible to put rabbeinu tam tefilin during ben hashemashot for one who puts it everyday but couldn’t put it earlier in that day , as not to lose the mitsva?
Yes. Although one should try to do this before Shekiya, if one was unable to he can do so during bein hashemashos.
See Shulchan Aruch 30:2 and Mishnah Berurah; Biur Halachah s.v. veyesh lehachria (concerning the berachah).
The Chayei Adam (14:15) actually writes that one can recite the blessing over Tefillin during Beis Hashemashos, and this is ruled by make authorities (see Artzos Chaim; Nidchei Yisrael Chap. 6; Yabia Omer 7:7), and this is the principle halachah. However, for Rabbeinu Tam Tefillin this is not relevant, since a berachah is not recited in any case.