When we have folder structure inside a document library, it is difficult to check all the files at single time. because it shows all the folder instead of files to users, by default SharePoint takes the items(folders) to check in without the items inside it. There is a very nice way to achieve this by creating another view. so that views can be switched whenever the users wants to check in multiple files. Here is the way:
Step 1: Go to document Library. Create a new view:
Step 2: Create standard View:
Step 3: Give a unique name to the view:
Step 4: Scroll down and give the folders filter as shown below and then save it.
Step 5: Now you can switch the view to find all the items without folder:
Step 6: Now all multiple files can be checked in without any issues inside folders: