I think I've figured out why my V4s suddenly disappear when I install new VBs.
I just finished installing a new V5 (announcement to come later!), and low and behold, it did the SAME THING for my V4s in V5 itself. The issue, I think, is that all of my installers are on an external hard drive: maybe V4s have a different way they store information? Maybe when I install another VB when that hard drive isn't plugged in, it scans but can't find the info, so it just... un-installs? Last night, going to install Kiyoteru, I transferred his files to the external hard drive and then installed him from there; V5 and Piapro both handled the new installations just fine.
I dunno. I'd like to think that's it. It's driving me up the wall. And this isn't an issue I've always had; it only started happening around the time I started storing my installers on a separate drive...