Checked-out is a status given to files that have been downloaded that alerts users that the file may be outdated. To clear the checked-out status, a file can be replaced (see above for replacing instructions), or files can be manually marked as checked-in.
To mark a file/files as checked-in
Head to the Files screen and navigate to the checked-out file(s) you wish to mark as checked-in.
Select the file(s) you wish to mark as checked-in.
Click Mark as checked-in if it appears in the action bar, otherwise, click the More actions menu button, then select Mark as checked-in.
A confirmation dialogue will appear alerting you that the file(s) and its references will have their checked-out status cleared. Select Check in when you're ready.