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John Zachariah
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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

John Zachariah
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