Sorry about my ambiguous description. 
Here is what I wanna do. Normally I use Python code to insert/update data of
two tables in my sqlite database file: *map and images*, table *map* stores
the indexs of pics, while table *images* stores the contents of these pics.
My Python code works well, untill the db file grows too big: I find some
pics I insert into the db file is incorrect,  then I rerun my Python code to
update these pics with right ones, but the select result of table images is
still not right. So i use command-line tool to test it, and there goes my
problem, I find the update/delete operation not working or giving any error
message, while I can still insert data into the same file.

>> Are you trying to use the CLI <while> the Python script is doing inserts?
Of course I use the CLI after my Python script finishes all inserts,
otherwise the db file is locked and all my operations in CLI would retrun

>> If you do ".changes on" before running the query, does the reported
>> change count increase?
I can't find this command in my CLI, and I use count_changes,  here is the
schema and my commands. I think my delete operation returns correctly, but
after delete, the select result confuses me. 



As you can see, insert works, and I can also delete/update this last
inserted record. It seems some pages of my db file is locked or something.

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