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Deleting a table manually in MySQL Server should not affect the running of the server itself but there could be a number of reasons why the server is not running. Some possible reasons might include:

1. Corrupt data files: If the MySQL data files become corrupt, this can cause the server to fail to start.

2. Incorrect permissions: If the permissions on the MySQL data files are incorrect, this can prevent the server from starting correctly.

3. Lack of disk space: If there is not enough disk space available to MySQL, this can cause the server to fail to start.

4. Configuration issues: Incorrectly configured MySQL configuration files, such as "my.cnf" or "my.ini", can prevent the server from starting.

5. Port conflicts: If another process is using the same port as MySQL, this can prevent the server from starting.

If none of these are the reason why MySQL server is not running, it might be wise to check the MySQL error logs for more information about the issue.