I have stopped recommending Lemmy to people, bc I would be embarrassed for a new user to come here, get bullied as I have been (far more than happened on Reddit), and blame me like "you recommended me to talk to that crowd!?"). Kbin.social was different bc those communities were blocked from the start - at an instance level even - though that server has been down for days, and now I see it's back up and full of advertisement posts as usual, bc many mods abandoned their communities due to all the technical problems with the service.
But there is hope for change in the future, in terms of perhaps making getting dunked on an opt-in rather than as it currently is an opt-out feature delivered to members of the Fediverse with little to no warning. e.g. here is a discussion I had with an instance admin. Progress, since so many of us joined the Fediverse since the Rexodus, has been (understandably) slow, but can happen, if we work at it!
This is a bit of a tangent though - OP was talking about instances, which at least one person said was removed deliberately so as not to overload them - so presumably by their own consent and likely even request?
Whereas here you are talking about communities, which should be visible across the Federation regardless - subject to the standard, complex set of rules (which you are working to lower the barrier for with all your alts pre-subscribing:-).
And to complicate matters further, it sounds like these communities have been missing from that list for many months now already. So this truly might be a unique situation, if that instance has actively removed consent to be listed there? Perhaps they would reconsider offering their consent to listing the communities if asked though?