Anything I say is just speculation at this point but I'm fairly certain large box sets, ESPECIALLY ones that come in specially designed cases or displays (like RockCan or earlier the Wizardry box), just don't get reprinted. I think that 2 year print run thing you always see (or used to see?) on albums was always the "we'll print more copies and make more on demand up until <this> date but after that we're done". I don't think specially designed box sets ever really follow that logic because everything about them costs more -- production, marketing, distribution, warehousing, shipping, etc.
A good example of how this works was the old Suikoden box set that Konami wanted to publish. They wanted to see how much demand there was for a Suikoden box set and said "if we get 1000 preorders we'll make 1000". There weren't enough preorders, so they ended up cancelling it. I've never seen a company poll like that before but I imagine that every company has to go through that kind of logic before making a box set like that because they'd largely be a revenue loss with the cost of production and how few people buy them.
tldr: box sets are always hard to come by. If you really want one you really need to find a way to preorder/special order or get it as quickly as possible because there is no guarantee they'll be around later. See: Breath of Fire Box Set, Rock Can, SaGa Premium Box, every DQ Box set ever, etc. I mean, even the Ghibli ga Ippai box set I have from like 1996 is still hundreds and hundreds of dollars and everything in it's been printed and reprinted individually like 3 to 4 times. It's either that or attempt to navigate the ebb and flow of the secondary market and various vgm speculators out there.
In the forever I've been collecting vgm and buying box sets I only ever remember one being widely available after it's release and that was the Castlevania box set that randomly got price dropped 50% on amazon.co.jp to something like 6500Y from the original listing price of almost 200000 and I have no idea why or how but a lot of people took advantage of that. That, and the one time I accidentally bought a second DQ box set and sold it to Ramza because I held on to it until he got enough money for it, lol.