This problem only affects the Android version of Threema under specific versions of the Android operating system.
Some Android versions (Jelly Bean 4.1.1 is usually affected, and on some Samsung devices even more recent versions) have a bug that affects paid apps. The sync account is lost after rebooting the phone; consequently, the contact synchronization does not work anymore. We’re currently searching for a reasonable workaround and recommend all users to update to a newer operating system version if possible.
As a temporary solution, you can turn the synchronization off and on again in the Threema settings. This will cause the account to be recreated and the synchronization will work again until the next phone reboot.
More information on this Android bug can be found here.