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It's been reported that this is a known issue with v1 of FMS12. FMS is able to get past te error and resumes a proper progressive backup of the file, which is what you are seeing.
Thank you for the information!
If this were your server, would you feel confident that there isn't anything genuinely wrong in this situation? If not, is there anything you would suggest I look for to ensure everything is working properly?
Also, any suggestion how to avoid the excessively large number of error emails from the server? I obviously do not want to turn off the email alerts, but I'm afraid I'll miss a genuine error message if I start ignoring these.
The only thing you can do is check the validity of the backup: restore a progressive backup to another machine and see if FM reports any problems with it. Also keep a good regime of regular backups.
error emails: you could disable the FM built-in emailing for now and set up an independent event log monitoring service. There are a couple of good free ones for Windows. You should be able to configure those to report back just the errors and warnings you want.