Your data is stored in the remote- not the TIU. Provided both are just set to TIU 1, only TIU specific settings matter- example variable channels set to fixed or other channel specific settings.
Edit- again, for the most part 99% of all your settings and data are in the remote. This is opposite to Lionel Legacy 990 for example or in theory BASE3 which in Lionel's system the base has the info. I think the MTH system works better for me when going from home layout and taking an engine to club layout- MTH I bring my engine and my remote and since both are TIU #1, the remote doesn't care it's not "my" TIU at club- everything works.
I also realize you are concerned about switches. Again, the AIU (which you did not mention) has no memory or storage so it's not storing anything. And, it is connected to the TIU, but the TIU is largely providing power for the AIU logic across the cable and a path from the remote to the AIU.
This is why- there is a way to backup or clone a remote- but you don't see backup a TIU or AIU in the DCS loader app.