What is "Init for Update" thread state in mariadb?
UPDATEing or DELETEing all of a big table takes a long time.  It is busy copying over every row in case of rollback.  Wait.

Is there some reason for using a sequence instead of an AUTO_INCREMENT?

Is there some reason for renumbering the table?

Neither of those is needed in normal MySQL operation.

To leave the existing column intact, but add a new id that is the PK:

ALTER TABLE t
    DROP PRIMARY KEY,
    ADD COLUMN id INT UNSIGNED NOT NULL AUTO_INCREMENT PRIMARY KEY;