There's no point in speculating here. If some third party tool is able to fuck with references in the
SL database itself that's a glaring exploit that serves no one in
SL by asking about it in a third party forum that few
SL developers look at.
There's no point asking us, we don't program
SL, we can't tell you anything beyond what we know about its infrastructure, which says the situation you've said is impossible.
But admittedly
SL is swiss cheese, so that's my point in saying: don't ask us, report it.
BUT I can assure you if your report begins 'OMG SOMEONE STOLE ITEMS OUT OF MY INVENTORY' like it did here, you're probably just going to be ignored by LL.