I will give a short introduction by tracking back a few lines before the Gemara which relates to the Rashi which you cite.

The Gemara states "Ella lav b'Shtei Eiduyos ..." and afterwards states ""Aval b'Edus achas b'Bas Achas Lo". Rashi explains that they testified in one shot that on Sunday he stole, and on Monday slaughtered the animal. They were then proved to be Eidim Zomemim concerning the testimony for Sunday. (i.e. witnesses said that they could not have seen the slaughtering on Sunday because they were in a different place at the time).

The Gemara now attempts to claim that Rabanan maintain that an eid zomem only becomes invalid from the time of his invalid testimony and onwards but not retroactively. They were proved to be zomemim from the time of the slaughter onwards but not for the testimony on the stealing.

Now to your Rashi. Rashi's title is what the Gemara states that since they were not proved to be eidim zomemim on the theft, therefore their testimony on the theft is valid.

(1) Rashi explains "v'Af Al Gav d'Behadi Ashidu Lay" - even though they gave the testimony about the theft and about the slaughtering in one shot, i.e. in one statement with no gap between speaking about the theft and speaking about slaughtering -

(2) "Ha Lo aschil pesulihu may hai shayta" - they did not start to be invalid from the time they testified about the theft (because they were not proved to be zomemim on the theft testimony).

(3) "d'Neima af al gav d'Ah echad b'Shabbos lo itzam" - so that we should have said that even though they were not proved zomemim for what they said happened on Sunday -

(4) "Mihu Sha'as Eidusan Sha'as Paslus Hoysa" - nevertheless at the time they gave testimony on the theft they were already invalid.

i.e. Rashi is explaining that we do not say that since the testimony on the theft and on the slaughtering was given simultaneously, even though they were not proved zomemim for the theft, nevertheless they are considered invalid for the entire testimony, but rather we say that they are only invalid from the time of the invalid testimony (slaughering) and onwards, and not from before.

Kol Tuv and a kesiva v'Chasimah Tova

Dovid Bloom