What does the sentence:
It can't have been her you saw yesterday: she is abroad.
become in indirect reported speech?
He told me it…
can't have been (?)
couldn't have been (?)
… her I had seen the previous day because she was abroad.
Both alternatives are perfectly valid. It simply depends on the emphasis the (later, reporting) speaker wants to convey.
That's to say if the reporter is particularly interested in the fact that the original speaker thought that at the time (or is misguidedly influenced by pedantic grammarians' "rules" which conflict with natural usage), he'll use couldn't have been.
If, on the other hand, the reporter is concerned with the implications of that earlier assertion for the current situation, he can quite naturally (and correctly/grammatically) use can't have been.
This principle can equally be applied to the supplementary justification, which would normally be adjusted to agree more with the initial verb form (couldn't have been ... she was abroad, or can't have been ... she is abroad), unless it's known that she's no longer abroad.
Note related usages such as “He didn't know where New Jersey was”, previously covered on ELU.