Lately I have been struggling to keep my total equipment inventory under 2900 pieces. This of course hinders my chances of playing full Crazy Orders sessions since I have to manually keep track of what I am picking up in any given run. I also seem to have confirmed my theory that downloaded Mii fighters were the culprit to having a lower maximum on equipment. In a recent Crazy Orders run, I was extra careful not to pick up any treasure chests in the final battle and managed to have 2997 pieces of equipment when the run was over. This is higher than the 2991 figure I used when I originally created this topic, back when I had a few downloaded Mii fighters with equipment, which have long since been deleted.
So what does this mean? If you truly want the ability to hold 3000 pieces of equipment, do not download Mii fighters online which have any equipment. Their equipment essentially gets mixed into your total pool invisibly, but you cannot share their equipment with your other fighters. Therefore, downloaded Mii fighters with equipment are actually lowering the ceiling you can achieve by poisoning your equipment pool with what I call "invisible equipment." They never show up on the selling screens since they are in use, but you cannot de-equip them either. Thus, deleting these Mii fighters is the only solution to regaining your potential cap of 3000 pieces.
On the other hand, you can have downloaded Mii fighters created by others without equipment, and those will not interfere with the ceiling of 3000 pieces of equipment. In fact, I had a handful of such fighters when I hit 2997 just recently, so they did not interfere at all.
Bottom line? Be very frugal with the Share features online if you want the ability to hold 3000 pieces of equipment or if your inventory is so highly optimized that you cannot afford to have equipment mysteriously vanish. There are still other situations when equipment vanishes, and these glitches are still not completely ironed out yet. But as long as you disable the ability for friends to send you stuff and as long as you sparingly use Share features online and as long as you avoid undoing sales, your inventory of equipment has a significantly higher chance of staying under your control.