If I have X number of jobs queued in FME Server (e.g. maybe there is a licensing error, or engines crashed), when I restart FME Server will all the jobs still be in the queue so that I can successfully process them?
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Yes, all the jobs that were listed in the queue will still be there when FME Server is restarted!
When jobs are submitted, a record is stored in the backend database. Upon restart of FME Server, the records will be fetched from this table, and the jobs can be processed once engines are available.
*Note: This was tested with FME Server 2015.1.3.2 Build 15575