First and foremost what version of FlashFXP did you upgrade from?
What version of Windows OS are you using?
Now; Assuming you're using v5.0 and newer the upgrade process should be completely seamless and automatic; preserving all your settings, site profiles, and custom commands.
If not then maybe there's something wrong with your v5.x installation and/or Windows registry entries for FlashFXP.
Create a full config/sites/command backup.
1. Start FlashFXP
2. Navigate via the main menu > Tools > Backup / Restore Configuration > Backup
3. Save the file some place outside of the FlashFXP program or data folder, such as your desktop or documents folder.
Removing FlashFXP
Uninstall FlashFXP. (During uninstall there is a question asking you to remove all data files, you can select NO)
Download FlashFXP from our website
https://oss.azurewebsites.net/download/now
Run and install FlashFXP. (If you checked the box to launch FlashFXP via the Installer, Close FlashFXP. This is important)
Start FlashFXP via the Start Menu, Quick Launch, or Desktop shortcut.
Restoring your FlashFXP configuration
1. Start FlashFXP
2. Navigate via the main menu > Tools > Backup / Restore Configuration > Restore
3. Select the previously created backup file and check all settings to restore and click the Restore button.
4. Close FlashFXP and restart it.
If you follow the above steps you shouldn't have any issues with installing software updates.
Or if you were upgrading from an older version then you probably missed this
Important information when upgrading from FlashFXP v4.x to v5.0