Here’s a real quick and dirty way to check in all files using SharePoint Powershell.
Get the SharePoint Web application where the doc library sits.
$YourSPSite = Get-SPWeb https://sharepointweb.domain
Get the Document Library from the root (or as many sub layers as needed)
$DocLibrary = ($YourSPSite.RootFolder.SubFolders["Name of Folder"]).SubFolders["Name of Nested Folder"]
After this call the checkin method for each file that is not in a checked in state
$DocLibrary.Files | ?{$_.CheckOutStatus -ne "None"} | foreach {$_.CheckIn("File Checked in by Admin")}
If there are even more subfolders within this folder, they have to be taken care of by simply adding a nested .SubFolders call .EG.
$DocLibrary.SubFolders.Files | ?{$_.CheckOutStatus -ne "None"} | foreach {$_.CheckIn("File Checked in by Admin")}
At this point it doesn’t matter what the sub folders are named it’ll go through each of their files within that “layer” of nested folders.
Hope this helps someone