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Your best option is to do as Jancawa said.
It is as smr1957 said. Four free creations now have the same status as three former addons from LE times. All 7 of them altogether are now deeply integrated in the base game. So removing any of them is a bad idea.
But OP does not want to restart his game, so with that in mind removing mods (or cc-files that act like mods) is not a solution.
@OP
Depending on what you want you can either give yourself items with console or use it to progress the quest. Items adding should be fine so long it is not some unique item bound to main-quest. Quest progressing is a bit more delicate procedure but you can find instructions to find ID, stage and set it if you google.
edit: this one https://www.nexusmods.com/skyrimspecialedition/mods/45181
Also, something worth to mention; the root tunnel is - AFAIK - only visible if you have "investigate the sewers" objective in the quest journal.