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To solve your problem i think taking a look at crouton project might help(requires putting your device to dev mode(not developer channel, developer mode))
Since i don't use my phone other than some social platforms(whatsapp & wechat generally) i don't need to backup my phone occasionally(and never tried it tbh), so i can't say anything about it. As long as i know crostini is only allowing your device to connect through 9p file system protocol which is might be the reason for your problem, i would try something like syncthing which is a foss syncing program connects your phone wirelessly through sshfs and backs up automatically
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