I bumped into your blog this morning--reading your posts goes well with coffee, albeit with the occasional erp-laugh spillage :-)You address two time lines by talking about each as a separate story line. If you've got characters in the here-and-now you'll need to tell me what they want and what's keeping them from getting it; what's at stake in their quest.
You provide an opportunity for readers to ask questions, so here goes: How do you recommend I address two time lines in a query?
To date, I've only addressed the main character's timeline. With queries limited to ~300 words including greeting, pitch, and bio, it's hard enough to grab the agent's attention with one timeline. I believe the essentials of the query can be communicated via the MC's timeline; will a second one surprise the agent when they (if they) ask for a partial or full ms?
Then you do the same for the characters in whatever the other past
The best way to figure out how to do this well is find other books with two time lines and look at the flap jacket copy for the book. You don't need to reinvent the wheel, just adapt it to the kind of vehicle you're querying.
I can think of two examples off the top of my head: The Dollhouse by Fiona Davis
and The Magpie Murders by Anthony Horowitz.
The comment column will no doubt have a few more good suggestions, and your local librarian is a resource you want to avail yourself of as well.
As to your question of whether an agent will be confused, the answer is no.
You can't put everything in a query, and a query is NOT a synopsis.
The purpose of a query is to entice me (your reader) to dive into the pages.