Yes, you can right-click on a folder, and select Check in.
Hi Phil, yes, by multi-selecting all the folders in the root of the vault, you can right-click and select check-in.
Note: depending on how many files you have, the process may take a while. I recommend performing this task during off-peak hours.
Note also that if you have selected to not allow duplicate filenames, but you do have duplicate files to check in, those duplicates will fail to check in.