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I was dropping some unwanted tables I have in the MySQL. When I run a drop table, its showing table doesnot exists. But when a check in the data directory, the .ibd file exists and its almost 1GB. How can i free that space/drop table now ?

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Reset to default
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You can go to the OS and drop the file because the data dictionary in the system tablespace (ibdata1) does not know of the .ibd file's existence any more.

I wrote a post 2 months ago about deleting temporary .ibd files : temp table (#sql-7a87_230c32.ibd along with its .frm) still exists on slave. It applies in your case as well.

Give it a Try !!!

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