Is there any possiblity to configure/customize fme server error messsages on server side? Any good idea for this?
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Other than English, FME Server is currently available in German, French and Spanish, though "not all components might be translated". If those are not the languages you're after it'll get trickier.
For error messages in workspace logs you can do custom log messages through the Logger transformer of course, but you don't have a way of intercepting FME's normal logging.