My sympathies, I know the feeling.
.
I'm going through a similar issue, but probably not as expensive as yours.
I recently needed to get new tires on the front of my XJS due to a
ball-joint
problem; I replaced the joints. I needed to replace a really bad tire
with the
spare to get me to the tire shop, and in the process I noticed the spare
was nearly flat, so I filled it before installing it, and threw the bad
tire&wheel
in the trunk.

After the tires were changed, the guy at the tire shop said he couldn't
close
the trunk lid after putting old spare into the trunk... turned out the
bottom
of the trunk was pushed up about 4 inches in the area where the spare sits,
that damage pretty well concealed by the carpeting.

I have no idea how that huge bump occurred, but I'm the only driver so
I surmise the car was damaged in a repair shop at some point (someone
tried to jack the car up in that spot, maybe, or it fell onto a jackstand,
and they let the air out of the spare in order to "cover" the damage
so I wouldn't notice it?).

I can't prove the tire shop did that, since the spare wasn't in place when
I arrived there, and it was soft when I removed it. I was not able to
pound the trunk floor back into position,  so it looks like I'm in for
a collision shop bill.