When files are open in desktop app, they are automatically checked out.
If they are open in desktop app. this is to modify the file, so the check in should be automatic, otherwise it will never been done, and files are stocked locally instead of to be pushed in Projectwise Web
The latest PW Drive version will automatically check out and check in files: https://communities.bentley.com/products/projectwise/f/announcements-forum/227756/projectwise-drive-2022-01-328-0-released-for-general-availability