Your main question is the dilemma… but I really want to work it through with you as this is the main question of all indoor growers and I really don’t have an answer at the moment…
I grow outdoors, so lets start there… My pots have the root balls in all winter and when I pull the plants out come spring there is no root ball… any roots in the soil I leave as to me it will be more carbon…
I am tagging in @organicgrower4m he is living soil and indoor… I feel (only my thoughts) that if you pull the root ball and lose soil just mix more in and start your teas etc over again…maybe at a conditioner at the most… I am just about to go indoor with my soil recipe so this is what I would do for now or until I learn otherwise…lol…