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The issue refers both to Service and Desktop refresh.
I'm using on prem SQL server as a data sources. There have been several cases when following a refresh, some of the data is missing while it exists in the source. The issue in Service usually gets resolved automatically with the next refresh. The issue in Desktop sometimes persists for longer.
I found several old threads describing more or less similar problem (although the data sources are different) and I'm wondering if it is possible that this issue still persists?
https://community.powerbi.com/t5/Service/Incomplete-data-after-refresh/m-p/540142#M55360
https://community.powerbi.com/t5/Service/PowerBI-Service-cannot-get-full-dataset/m-p/475237#M49646
https://community.powerbi.com/t5/Desktop/Power-BI-Desktop-Query-Not-Fully-Loading/td-p/479974
@Quiny_Harl , where these refresh successful. Also check if there is timezone difference between the service and the on-premise database.
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