For the most part, the OneDrive app will display what is returned from the OneDrive Server. If your folder contains any of the following characters, it will not be displayed:
Double Quotes “
Angular Brackets < >
Slashes \ /
Changing the folder name to remove the special character should allow the folder to display.
Also, there is a limit on the OneDrive/Office 365 side. I believe that by default the limit for items to be returned is 5000 folders and files.
There are a couple options to work around this limit. The OneDrive administrator can increase the default limit to allow more folders to display. Or you can combine files and folders to reduce the number of high level folders in the account. This should allow more folders to display after logging in.
Please let me know if any additional questions come to mind.