MySQL InnoDB .ibd file growing extreme
Study your queries.  It could be that you accidentally have a "cross join" because you left off the ON clause.  This could lead to a huge temp table that, in certain circumstances, could bloat the .ibd file.

What version of Percona?

How much RAM do you have?? innodb_buffer_pool_size =  650GB implies that you have at least 700GB!  Otherwise, you will swap to death.  (This won't explain the .ibd issue, but it is a serious one.)

These are also rather high unless you have a lot of RAM:

thread_cache_size = 256
table_open_cache = 10000
max_connections = 10000


Please provide SHOW CREATE TABLE for that one table, and SHOW TABLE STATUS for it.  BLOBs and TEXTs are of interest; other things may be of note.

A query would take a long time to bloat the table.  Glance at SHOW FULL PROCESSLIST; you might spot it.  And/or, turn on the slowlog, and check it later.

A query (added from comment)

select  table0_.id as id,
                table0_.created as created,
                table0_.modified as modified,
                table0_.chunk_index as chunk,
                table0_.content as content,
                table0_.other_table_id as export
    from  table table0_
    where  table0_.other_table_id=8305
    order by  table0_.chunk_index ASC


To improve the performance of that query, you need INDEX(other_table_id, chunk_index).