So today Rob and I discovered that it is possible to work with Windows Powershell in the Office 365 environment, using the Microsoft Online Services module. We decided to follow the instructions and install the necessary components. Following some basic commands we were able to perform some basic administration on users, such as, changing display names, contact numbers and names.
However after some more research into the matter, Rob discovered that the data being changed by these commands was the data held in the main Office 365 user profiles, and not in the SharePoint user profiles. This is why we were not able to access the custom user properties that we had created to handle the extra functionality of the annual leave process. However, this should be possible when using SharePoint Server 2010 instead of SharePoint Online with Office 365.