the eaccelerator cache is just a folder on your server. The exact location of the folder will depend on the settings used in Apache and PHP. You may be able to find the location if you look at the Moodle's "PHP Info":
- Administration -> Site administration -> Server -> PHP Info
- search for "eaccelerator.cache_dir"
Once you know where the folder is you need to clear it out - not delete it
The method you use to clear out the folder will depend on who is clearing it out, and the tools that are available. For example, if you have SSH access to your Unix/Linux server, you can clear out the cached files with a command like this:
rm -fR /path/to/eaccelerator/cache/*
On one system that I run, I have set up a cron job (=scheduled task run by the operating system) to remove files from the eaccelerator cache that are more than two weeks old. The command looks like this:
find /path/to/eaccelerator/cache -atime +14 | xargs rm -f