Content Matrix does not have ability to check in files before migration, this can only be done on Sharepoint level.
Here are the steps to check in files before migration
In document library, do the following:
Settings - Document Library Settings.
Under Permissions and Management click on Manage checked out files.
This will list all the check out files and if files were choose to check out files, please take ownership and check the files back in.
Migration Assessment Scan Checked-out files - Migrate to SharePoint and OneDrive | Microsoft Docs
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