I used to work at the Disney Reservations Center. When you make a booking through a
travel agency, the reservation belongs to the agency, not the individual agent. If you
travel agent moves to a new company, she or he shouldn't be taking your reservation unless both you and the original agency agree. As that didn't happen here, you will need to take a few steps to fix the problem.
First: Don't panic. While it's technically possible that the agent will scam you, that's a fairly serious crime. Based on the information provided, it doesn't sound like you are in danger of losing your money.
Second: Gather all your information (like both confirmation numbers) and call my former colleagues at the Reservations Center. Let the Cast Member know that you are concerned because the travel agent you are working with seems to have switched travel agencies without informing you. Provide the name of the (original) travel agency and ask if your reservation is booked under that name. You should be able to get that information.
(Hint: If the Cast Member seems confused, she or he might be fairly new. This is a bit of an unusual situation. If you get any resistance, ask to speak to a Supervisor. Make sure you say "Supervisor" and not "Manager". Those are two different roles. Managers manage people; Supervisors fix reservation problems.)
Third: If your reservation is still listed under the original travel agency, you're probably okay. However, if the travel agency has changed, ask to speak to a Supervisor (if you're not already talking to one). Ask about your options. Honestly, I'm not sure what those options will be. My best guess is that someone will want to call the original travel agency to verify that they agreed to let the agent keep your booking.
If the Supervisor asks for your contact information and says she or he will call you back, that's normal. Sometimes these thing take time to figure out. Once you call, all sorts of notes will be added to your reservation. That's a good thing, as it will protect you.
I'll echo the sentiment of other folks: I'm sorry you're having to deal with this issue. But, don't panic. Just call the Reservations Center and ask for help.