If it were me, I would:
1) Contact the maintainers of the other repositories.
2) Draft a DMCA counter-notice, laying out that:
"The repository was open-sourced by Dmitry Yusupov who is co-founder and CTO of Nexenta. This was publicly advertised on multiple public forums, including [], as well as the github repository itself. As a CTO, he had either authority (or, at least, apparent authority) to open-source this tool. This tool continued to be publicly advertised under a [insert license] license by Nextenta for [insert number] months in Nextenta's official github repository.
I cloned this tool in full compliance with the license under which Nextenta licensed this tool, and continue to comply with this license. Whereas this license has no expiration clause, Nextenta has no legal grounds under which to withdraw the [insert license] license under which it licensed this code to us.
I, and others, have invested significant time, cost, and effort, in reliance on Nextenta's advertising. In addition, Nextenta's business has generated significant value from the goodwill from their announcement of the open-sourcing of EdgeFS. Nextenta has no grounds on which to retroactively withhold continued rights to users who use their code under this license.
Shutting down this repository causes ongoing harm to myself and to [others who have signed on] and continue to rely on this repository for [whatever value you derive].
If Nextenta believes its CTO and employees were not authorized to take this action, Nextenta's recourse is to seek damages from those employees. It has no grounds to retroactively deny rights to [list of people]. If it chooses to do so, [standard language about seeking maximum damages, expressly reserving all rights, etc.]"
Find legal language online in other such filings, and stitch it together. Try to understand what it says and why.
3) Chip in for a 1-hour consultation with a GOOD lawyer (high per-hour costs, likely, but low time commitment). Have them revise this letter. Good lawyers can do this FAST. Note that you want to have EVERYTHING organized and lined up going into this meeting. The more time you spend beforehand, the less you'll need to pay the lawyer. That's the point of the draft.
4) If you have sufficient funds, have them ship this letter off on their letterhead (looks scarier). Lacking funds, do it yourself (still shows you know your rights).
Most companies will back down at this point. However, if they don't, these things can either get super-expensive (if you hire a lawyer) or completely life-consuming (if you decide to handle the legal work yourself). One upside is you do learn /a lot/ in the process either way. Lawyer friends who can help you unofficially are also super-useful.
I'll mention that's what I'd do. Most people would back down and get on with their life.
Another pressure point are an adversary's customers. Those are often awesome. If customers don't believe a company follows contracts, they're f-ed. Often, this just takes communicating what happened, but sometimes it needs to be adapted to customer culture. But you do need to be careful how you pursue this (again, being careful to stay well within the right side of the law).