This article explains how to exclude (filter out) lists or libraries based on their item count during migration using a PowerShell Transformer
List Filters based on Item count in the "Filter Options" tab of Content Matrix job configuration are not working as expected at the moment.
While Quest is actively working to address issues, customers are encouraged to leverage this alternate method of using PowerShell Transformation to achieve the same benefit.
Use the transformer in the attached package in your migration job. A README file that explains how you can modify the PowerShell code to alter the filter logic is included along with examples and instructions.
Generic graphical instructions on to add a transformer to a migration job are available in the link below:
How to add a transformer to a migration job
Note that this particular transformer needs to be applied on "SharePoint Lists" definition as shown below:
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