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I am aware that you don't want to remove the innodb tables from /var/lib/mysql for a linux distro of mysql (I have Ver 14.14). So I used the command

drop database mydb1; 
drop database mydb2; 
-- etc

but see that the folders mydb1 and mydb2 etc. are sill in /var/lib/mysql, and the .MYD, .MYI and .frm files are there in most cases. Are the database folders safe to manually delete now? I know the innodb files are very sensitive.

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First, MySQL latest version is 8.x.x, so it's impossible for you to have 14.x, check that.

Second, maybe your data dir is not /var/lib/mysql. To check this variable run the following script and check the actual datadir for your instance.

mysql> SHOW VARIABLES LIKE '%dir%';
> +----------------------------+--------------------------------------------+
> | Variable_name              | Value                                      |
> +----------------------------+--------------------------------------------+
> | basedir                    | /usr/local/mysql-max-4.0.13-pc-linux-i686/ |
> | datadir                    | /usr/local/mysql/data/                     |

Also check for any errors when you run the DROP DATABASE sentence.

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