The initialize option currently still requires that the table is valid (this is a known issue, planned to be updated in a later release). Right now, it just clears out anything other than the default "All OSSEC Servers" entry.
The simplest thing would be to open the file in a text editor and replace its contents with:
"ossec_server",description,managed
"*","All OSSEC Servers",0
Then, run the Rebuild OSSEC Server Lookup Table search again. Alternately, you can manually add a line for your server while you're editing the file, e.g.:
myserver,"This is my managed OSSEC server",1
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