I'm looking to buy an audio interface for recording guitar. I'm planning on splitting my signal chain into 2, with 1 channel going direct into the interface using the line input, and the other going to mic'd up guitar combo. However the interface I plan on getting has dual inputs - XLR/TRS in a combination. Phantom power can only be turned on to both inputs so therefore there will be phantom power going to the TRS line input. Will there be connection from the TRS output meaning I could damage my guitar/effects through unwanted power?
Normally the phantom power would only be present in the XLR inputs of the interface. For example, the Focusrite Scarlett, a very wide spread model in the market that has combined XLR and TRS connectors, clearly states in the user manual:
48V phantom power switch for mic inputs - enables 48 V phantom power at XLR contacts of both Combo connectors.
Note that if you insert a mono (TS) jack connector into the TRS plug, the tip and sleeve of the plug are going to be short circuited. If there was power on these pins there would be an actual short circuit. For that reason, TRS connections exist to provide compatibility with both balanced and unbalanced lines, but not to provide phantom power.
Anyway you should check the specs or manual of the specific interface, or inquire the supplier or manufacturer, to make sure that there is no phantom power on the TRS connection. That would be very unusual, but if it would be case with your specific device, you could not connect an instrument cable, not because it would damage the instrument, but because it would damage the interface.