Due to the way the upgrade processes, some applications may be uninstalled prior to the upgrade. In theory, the process retains installation data and will re-install the application after the upgrade is complete. But if it is an application that is unfamiliar, that processes may not work. The end result could be a Windows 10 install with applications missing or miss-configured.
More specific information can be found here:
The update that provides access to the Windows 10 upgrade is KB3035583. With this update installed, a new folder will be created at “C:\Windows\System32\GWX” and the program GWX.exe will provide a prompt to reserve Windows 10 in advance of the July 29, 2015 release date. Once reserved, the Windows 10 update will download automatically once it has been released.