I don't, obviously, have any absolutely concrete evidence for this theory. But there's some interesting clues in Daring Don't.

Daring Do: [grunting] Give it back, Caballeron!
Dr. Caballeron: That's Doctor Caballeron to you.
Rainbow Dash: [hushed] He's from book four: Daring Do and the Razor of Dreams. He wanted to partner with Daring Do on her adventures.

This bit is interesting for a couple different reasons. First of all, obviously, he wanted to partner with Daring Do on her adventures, which is straightforward, if not especially telling. The correction ("Doctor Caballeron") is more interesting. It implies, if nothing else, that Daring was less formal with him at some point.

But the plot thickens, I think, here:

Daring Do: I. Work. Alone.
Rainbow Dash: But why won't you let me team up with you just this once?!
Daring Do: My work always involves secrets. And since you never know who you can trust, it's best never to trust anypony.

I suspect that Daring Do was betrayed at some point.

We know that she was at least somewhat associated with Caballeron at some point.

I'm just sayin'. Something seems to have happened.

I've touched upon this in passing in my story The Lunatics, which features Doctor Caballeron as a main character. I'm not sure if you lovely Do fans would be interested in checking that out, but it does include action, adventure, and archaeology. I'm sure the pith-hatted pony would approve.