Unfortunately this game is "set it and forget it" without the ability to make in-game adjustments based on injury.
You can use overrides and set the depth chart but there is no ability to say
"If RT1 gets hurt then move LT1 to RT1 and play LT2 at LT1"
You can set the depth chart that way but IDK if LT#1 will play RT after an injury if there are other options in the depth chart to chose from.
Does the A.I. remove your starting LT if you have a RT#3 option in the depth chart?
You say you have an 86 LT#2....what is he rated at RT? I would look at making him the primary backup at both tackle positions.
I get where you are coming from but also think you are over complicating things....I never use overrides and just set my depth chart without using starters at multiple positions.....I have had plenty of success that way.
Sorry I can't help with the dilemma but would simply use the starters where they start and set backups for each position....If you get an injury in game....hope for the best and fix the depth after the game.
My concern would be the A.I.'s interpretation of what having multiple players as #1 actually means which might lead to one of the best players not even starting or it rotating positions every other play or something else that makes no sense.
For example you put your LT#1 at RT#1 too so it decides to play him at RT and now your LT#2 is starting.
Sorry, I'm not much help but I would start both your starting tackles and make the 86 LT#2 my primary tackle backup for both.