I was thinking that maybe the key factor to consider here is Cover being so tight-lipped. When Vesper was suspended, they released an official statement about it. When Rushia performed her Final Yab, they murdered her with extreme prejudice almost immediately. However, when it comes to Magni and Grandpire, they've said nothing except a short notification which basically said "err, yeah, they won't do anything for a while". It's been over a month since then and we still haven't got a single piece of new information. Now, what does that tell us? IMHO Cover either cannot say anything yet (as in, the BIG PROBLEM hasn't been resolved yet and therefore they can't exactly tell us anything because they still haven't reached the conclusion/solution), or they don't know what to say (as in, the BIG PROBLEM has possibly been resolved, but it was something so extraordinary they haven't decided how to proceed).
If the problem hasn't been resolved yet, then it's either because management royally fucked up on the top of the original problem, or because it's beyond Cover's power (for example, a police investigation being in process). If the problem is so weird that Nips have no idea what to do with it, then we might have found ourselves the actual fucking Rrat Mines of Moria, because the possibilities are endless, including failed gay romance.
tl;dr if the reason for their hiatus was something conventional, they would've already been fired or reinstated by now, so it's either a pile up of fuck ups, something incredibly complicated, or something wild, beyond our reasonable guesses