Hallo Ernesto, Different instances of Syncany (assuming different computer names!!) never access the same files on the server. Each instance/computer writes its own update file. So there are no concurrency issues here.
The only file that is written by multiple clients is the repository-* file. But since this only happens if new shared folders are added, it is very unlikely to be overwritten. The "downloading files" issue only occurs when the computer name of the "new instance" is the same as the previous one -- because syncany assumes that you are the same guy. Did that answer your questions? Cheers, Philipp
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