Sounds like she was just broaching the subject, not at all suggesting termination. She did what she could to let you know not to misinterpret the discussion. Trust her at her word. It is fine.

The flat affect when first starting lithium isn't particularly unusual and the it could just be coincidental and have nothing to do with the lithium. It's hard to know. Give it some time to settle in. It took around 5 weeks to get to the point where I realized the lithium had really kicked in and was working. I'm sure your pdoc will draw blood levels to check to see if you are at therapeudic levels.