Did you try increasing the limit? using this cmdlet
Set-SPBusinessDataCatalogThrottleConfig -Identity $dbRule -Maximum 1000000 -Default 3000
This Maximum value and Default can be modified accordingly
It is also noteworthy to mention below
"Remember that if you run one of these commands and immediately type $dbRule, you won’t see the changes reflected; you should re-fetch the rule using Get-SPBusinessDataCatalogThrottleConfig again. Your changes are immediately committed by Set-SPBusinessDataCatalogThrottleConfig, but it may take a few minutes for them to be reflected in external lists and other runtime scenarios."
Reference: BCS Throttle Management