We are sorry for the delayed response.
This is as-designed behavior. For data sources, for which dedicated accounts are not available, LastSyncTime is set to the end time of the run.
Dedicated Account option is available only for Salesforce, SugarCRM and Dynamics CRM. For other data sources, a non-dedicated account is used by default. This means that:
a) The first synchronization synchronizes all the data.
b) Any changes to CRM data performed during the synchronization operation are ignored. If the other side is a relational database, all the changes to it performed during the synchronization operation are also ignored.
It's highly recommended not to edit the data being synchronized during the synchronization operation.
c) Any changes, performed by the user specified in the synchronization package connection or any other user between the synchronization operations, are synchronized.
We have asked our developers to check if there are any possible solutions for your case (with Zoho CRM) and we will let you know results as soon as possible.