Let's just recap a few known things about TIUs.
#1 they need power to operate the internal electronics. There are 2 basic methods to get this power- channel1 fixed input the tiu logic can borrow power, or AUX power in, the little round coaxial power jack on the end of the TIU. So as such, you did not mention an AUX in power supply when describing your system so we assume that then means you must always power channel 1, whenever you want to use channel 2.
Ok, so let's say you knew that or already were doing that -always ensuring fixed channel 1 had power in- or you actually do have an aux power wall adapter plugged in. In other words, we know beyond any shadow of doubt the TIU has constant power and the red power light is on inside the TIU.
#2 Then, even a minor short, derailment, accident, can cause damage to the DCS signal generator portion of the TIU on a given channel. So it's entirely possible you damaged one of your channels- example fixed2, and so whatever track is connected to that channel might then have low signal- not be able to find engines and so on.
That leads to...
#3 You can swap tracks between TIU outputs. Giant Caveat here again is that the TIU must have logic power to operate. So again, based on what you have said to this point, TIU channel 1 input power must be on for your TIU to be powered and then what you would be doing is plugging in your outer loop to the TIU channel fixed1 output. Now if suddenly those same engines work fine on your outer track while it is connected to fixed1 output of the TIU- we begin to suspect you damaged TIU channel fixed2.
Again, as long as you follow the rules and the TIU logic internally has power, you could then connect and repurpose say one of the variable channels to then power your outer loop.
You can ignore TMCC/Legacy portion if you do not have it.
