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Most of the time just doing a simple mysqldump of one database then the sites actual files will work fine without any downtime. As long as you do site1db, site1files, site2db, site2files, etc (instead of dumping all dbs then all files) and the databases aren't massive it will be within sync enough. It's even less of a big deal if you keep multiple backups instead of relying on one. Sure to be technical you should lock it all before the backup then unlock it but it usually isn't a big deal for a normal site or small group of them on a server.
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