I'm sorry, but I can't see how installing/uninstalling Orlando could have any effect on other sceneries, under normal circumstances.
The most likely explanation is, your scenery.cfg was ALREADY corrupted before installing Orlando, and this might have confused its installer when it had to remove the Orlando entry when uninstalling.
That's why, our current FSDT installer have lots of checks on the scenery.cfg BEFORE installing the scenery, and don't touch it if any error is found, so people can't assume they caused problems, since they don't do anything until the preexisting scenery.cfg errors are fixed by the user. The Cloud9 installers probably weren't so "defensive" in nature, and assume the scenery.cfg is always clean, which is not always the case.
However, even Cloud9 installers make a BACKUP of the scenery.cfg as it was BEFORE installing them so, you could have restored the situation by simply using the backup file, which is located in the same folder as the regular scenery.cfg.