There is no need for calling eaccelerator_rm() there, eaccelerator_set() takes care of replacing the older value with a new one. That being sad, it's extremely strange that PHP timed out on that call, it simply shouldn't happen.
The only possible cause I could think of is that maybe eAccelerator is set to cache everything on disk, and the disk I/O was blocked for some reason, and thus eAccelerator couldn't remove the old value.
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