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Are there any limitations on when to run the updates, I seem to remember doing it once and it losing the data for the rest of that current day ?
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There aren't any real limitations on when to run the updates. The experience you had where an update lost a day's data was likely caused by running an import against an incomplete or missing xmltv data file. Prior to v1.15 of the importer, the first thing that happened when an import started was that the epg data in snapstream was dumped. Obviously, this isn't very smart. If no xmltv data is present (or the file is invalid) you've just dumped all of that useful data! With v.1.15 and later, the existing data isn't dropped until the xmltv datafile has been inspected to be valid.
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Is it ok to update with snapstream running, transcoding and recording ?
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All should run fine while snapstream is running. No need to shut snapstream down. The only problem you could run into is that the importer does require some CPU while populating the EPG database, and this could cause stutters during playback. I have my imports scheduled to run every night at 4am.