Asserting copyright infringement against closed source software using GPL code

In the US, B would have an opportunity to depose A and/or their staff about how the functions of B's code that seem like B's code got implemented before the case began to go to trial and to potentially get other discovery such as the source code to be examined under NDA by an expert. Assuming that A didn't give up under the threat of the discovery process uncovering their malfeasance, then they might not have used B's code at all and discovery might prove whatever A has been saying about that so far (hopefully through their attorneys). In which case, B goes home with their tail between their legs and is out attorneys' fees (maybe to both sides).

Getting to this point probably will cost dozens if not hundreds of attorney hours, and the winning side in a US copyright case can request costs from the court including their own attorney's fees, so it's worth thinking about how much this is worth to you. All this will happen in federal court before a most likely non-technical judge who will have to be convinced of the copying and probably not understand or know about copyright licensing or appreciate FOSS nor software development processes (if any were followed, see @Graham's answer).

B's attorney might have to lay this out for A's attorney, that their clients could both be out over $100k over a command-line parsing library for not following the GPL (or whatever), and see if they really don't want to open up their code or buy a license for, perhaps, less than the court case is likely to cost. B's attorney should make sure that's not extortion in their state.

A can reasonably demonstrate this without showing the source code, by showing their change control history (without the differences for each file, of course). Other documentation such as design documents and review records would also help. The aim is to show that a development process took place, starting from nothing, and developing iteratively until they ended up with what they have today.

Since B's code is GPL and hence publicly accessible, A must also have a quality process document describing their Chinese wall process to ensure A (or A's team) did not refer to B's code during the process.

If A does not have an appropriate quality process, and A's code "magically" appeared in their version control system overnight with no further documentation, A will have a great deal of trouble proving that they did not violate B's copyright.

Conversely of course, B does have to have a credible case to put to the court. Common ways for B to prove this would be by checking for common function and variable names within the object files, and checking for common text strings within the object files or executable. And during disclosure, of course any lack of documentary evidence for independent development would be considered too.

The important feature of any copyright case though is that it is a civil case. As such, there is no such thing as "innocent until proven guilty". The judge is expected to rule based on the balance of probabilities, and it is as much for A to disprove the allegation as it is for B to prove it.