REGEXP_REPLACE is matching but not replacing with empty string
UPDATE files 
SET files_name =
    REGEXP_REPLACE(
       files_name,
       '(S[0-9]?[0-9]?[0-9]E[0-9]?[0-9])([^0-9].*)',
       '\\1'
    ) 
WHERE type = 5;


fiddle

UPDATE


  I executed this command, with redacted info of course... 

mariadb -h ip -P port -D database -e "UPDATE files SET files_name = REGEXP_REPLACE (files_name, '(S[0-9]?[0-9]?[0-9]E[0-9]?[0-9])([^0-9].*)', '\\1') WHERE type = 5;" -pPASSWORD



You need to quote a slash: 


in command line 
in SQL query


So you would use '\\\\1'.

You may avoid using slash by using CONCAT(CHAR(92), '1') instead of '\\1' in the query text - in that case no slaches in SQL and quoting don't need in.