Is it consider a copyright infringement by both company A and company B? Are the employees in violation, too?

It depends on the license that Company C granted to Company A.

That license may permit Company A to engage in whatever conduct is necessary to extract the data that's resident on Company C's software. Which would include using an agent, such as Company B, to copy the software.

But maybe not. If not, then Company A is a vicarious infringer (either contributory and/or via inducement) and Company B is a direct infringer of Company's C software. The Company B employees who actually did the copying are typically not personally responsible unless they are in a management role with the company -- that is, the employee had the authority, and actually did, direct that the infringing conduct occur.

It depends on the full facts. There isn't enough information here to really work out what would actually happen. I'd want to see the license agreement and find out about any other contracts (verbal or written) between A and C that might indicate that C permitted or acquiesced to B's copying. Since we don't have those facts, let's go with what we have:

Because A hired B to perform certain work, B may be considered agents of company A and authorized under the terms of that license agreement to use the software.

Further, the terms of the license agreement may expressly permit or forbid Company B's use under the circumstances.

Also, the way that B used the software might be argued as "fair use" which is a legal defense to a claim of infringement. Whether this "fair use" is a fact-intensive analysis.

Regarding whether the employees or Company B itself would be liable for infringment - let's supppose that the acts of B were indeed infringing and C decided to sue.

In the eyes of the law, both B and its employees have infringed and violated the copyright. Under the doctrine of "respondeat superior" (which means essentially "let the master answer for the deeds of the servant"), C could come after B for infringement as well as employees of B. Chances are good that they'd target B, since companies tend to have deeper pockets than the individuals who work for them. Here, if C can prove that the principals of B had actual knowledge of infringement, they'd have a pretty good case.

There is also a colorable argument that B was acting as an agent of A, so C may sue A too (again, based on agency theory that B was acting under A's direction).

I'm assuming that this question is more than just a hypothetical situation, so depending on who you are, you may want to take the following steps:

If you are A, find out what your rights under the license agreement are (and any other contracts). You might want to "come clean" with C and let them know what happened, and ask them for their consent for how B used the software. C is in the business of selling software, not suing customers, so you may find them to be perfectly amenable to this sort of thing.

If you are B, talk to A and see if the two of you can work together in getting B's consent for the work done. you might drop some money for this but it's cheaper than court.

If you work for B, talk to your boss and share your concerns. See if the principals of B will work with A on the special license for this work.

If you are C, talk to A about the situation and see if you can work out a special license with them for this work. It's in your best interests to have A as a happy customer, and it sounds like B's only use was the conversion work. Doesn't sound like B is out to steal your software.

I hope this helps - the facts are kind of thin, so it's hard to really predict the results. If at any time you are unsure of your rights or possible liabilities, spend a few bucks on an attorney that can analyse the complete set of facts and help you sleep better at night.

See begining answer to your previous question.
Company B employees work under the direction of Company B management and under respondeat superior doctrine will attach liability to the company B. Nevertheless, each employee that performs an illegal act is personally responsible too. You cannot kill someone and defend saying that my boss told me to do it!!!.