I had a site mesh that was disappearing from all my views, although it was still selectable.
It turned out the explanation was because I had built up a lot of solid element operations over time, and one day one of them went Full Retard and made the entire site disappear. The trick was working out which one.
Here's what I did:
1) In the 3d view, turn on, and unlock all layers
2) Select the (invisible) site mesh.
3) In the Solid Elements Operations window (which is called "Edit Targets and Operators", when it's open, just to keep you on your toes), I clicked on the button labelled, "...Operators of Selected Elements"
4) I hit F5, which isolates only those elements in the 3d View
5) I analysed what was there, and found a few items where the SEO was no longer necessary due to modifications I'd made since then.
6) I removed the SEO link for those items
One column in particular was once embedded in the ground, but is now sitting up on a stirrup, and when I removed the SEO link for that one, suddenly my entire site came back!