I'm a little confused. I am making the following assumptions about your code:
1) You have implemented update collections as a DeviceJob i.e. an object of class DeviceJob
2) The BookSync code is also implemented as a DeviceJob.
3) The BookSync auto collections code first schedules a sync and then schedules a collections update job
In this case calibre will first run the sync and only after it is completed will it run the collections job.
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