What format are the books being read? ePubs or kEpubs purchased from Kobo?
If kEpubs purchased from Kobo and synced via either Kobo Desktop or WiFi then yes, Kobo will sync reading positions.
If ePubs whether loaded via calibre or ADE, or just copying files yourself, then no; reading location is not synced. You could look at using Kobo Utilities to sync, but I'm not sure how easy it would be to automate.
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