You can check in multiple documents at once using the Check In action in the Quick actions pane. We recommend checking-in checked-out documents before running a migration since checked out documents will not be migrated (only their last checked-in version will be migrated).
Prerequisites
You have site collection admin permissions on your targeted site collection(s).
Note: Site collection admin permissions are required even if you have higher admin privileges like SharePoint admin or Global admin permissions. For more info, see Microsoft administrative permissions.
Tip: To manage all your site collections, you can connect to your central admin or admin center with SharePoint admin, Farm admin, or Global admin permissions.
Index
How-To
Check in documents in one site collection
Select Explore from the sidebar.
Navigate to the document level of your desired library.
Select the documents you would like to check in.
In the Quick actions pane, select Check in.
You will be brought to the Options screen.
Select the type of version you would like to check the documents in as, and add a comment if applicable.
Click Check in.
Check in documents across the whole environment
Select All reports.
Click the Checked Out Documents report under Built-in reports.
Select your whole environment, or drill down and select multiple site collections.
Click Run now.
You will now see a list of checked out documents on your Results screen.
Select the documents you would like to check in.
In Quick actions, select Check in.
You will be brought to the Options screen.
Select the type of version you would like to check the documents in as, and add a comment if applicable.
Click Check in.