Hi Jamie,
Based on my search, I didn’t find some articles about using PowerShell or script to multiple checking in all the files. You can try using SharePoint designer for multiple checking in:
- Install SharePoint Designer 2013.
- File>Sites>Open Site. You can also navigate to the library, click Return to classic SharePoint>setting gear>Ribbon:On>LIBRARY tab>Edit Library.
- In SharePoint Designer 2013, click All files in the left panel>choose the library (choose it, don’t access it)>click Check In>OK.
As I mentioned above, you may exceed the list view threshold limit. You can mange the library to avoid exceeding this limit. Otherwise, it may cause some unexpected issues.
Moreover, as you mentioned the page refreshes in Content and Structure page, you may change to another browser to check the outcome. It may be caused by there are too many checked out files.
Best regards,
Tim