Spoke with @q.prestavoine and we got through this migration and update. Posting the steps below just so anyone who searches this out can see what was done.
First step was
git pull origin master
on the passbolt directory
Then edited the Migrations/20220809190030_V372ImproveFoldersRelationsIndexesAddItemsToUserTreePerformance.php file to remove the migrations that were stuck, in this case it was lines 17 through 41
Then did the migrations manually by running the following in MySQL on the passbolt database:
DROP INDEX foreign_id ON folders_relations;
DROP INDEX foreign_id_2 ON folders_relations;
CREATE INDEX foreign_id ON folders_relations (foreign_id, folder_parent_id, created);
Then proceeded with the update instructions from here