So, you changed the content of a scenerypackage, plugins or aircraft folder but in XO you still see the old content.
XO uses the TimeDate stamp of a folder to check if this folder needs to be (re)scanned or that it can be skipped. Unfortunately, if you add or change a file inside a folder the TimeData stamp is not changed and XO will skip it when scanning.
If this happens, just go the the Actions menu and select the rescan you need:
The 2nd option will only update the version information stored in version.txt files. It is a faster scan, although the normal full scan does not last too long since adding parallel processing to XO.