The 'Server operation too large' error occurs when a query exceeds the governor limits established by Salesforce.
Governor limits are usage caps imposed by Salesforce to prevent server issues and improve performance.
Pulsar, as a client application, has to use the standard API calls to query the data during the sync process. Governor limits apply to these queries. If you have Pulsar Settings installed in your org, you can apply sync filters and other sync parameters to reduce the number of records you are syncing. If you don't have Pulsar Settings in your org yet, refer to this page on how to install and set up these filters.
https://luminix.atlassian.net/wiki/spaces/PD/pages/48398341/2-4.+Data+Sync+Settings
Example log
[2020-06-15 11:32:07,579624][ERROR][1608] - Server operation too large (Attachment, wave 0)
[2020-06-15 11:32:07,579624][ERROR][1608] - syncCompleteQueryModifiedSObject failed (Attachment, 1150)
[2020-06-15 11:32:07,579624][ERROR][1608] - syncQueryModifiedIfNecessary failed (1150)
Note: The sample error message refers to the Attachment object but you could see this error against any object. You may also find this Salesforce article helpful for understanding the error: https://developer.salesforce.com/forums?id=906F00000008oleIAA