When you use the Physics solver to write animation data to an object, it writes the data into the Translation and Rotation channels of the object. For a Character it writes the data on the Control rig effectors.

If you do not want this to happen, store the animation you want to use in the solve in another Take. Then, use this take as an input and record onto yet another Take. (You can also copy the take and record over it.)

The overwrite occurs when you plot or record, and a dialog box appears to ask if you want to overwrite the current take. If you choose yes, and you are on the same track, your animation data is overwritten.