The following alert displays in the Part Navigator after an update:
Feature applied to different bodies since last update
Solution This is working as designed because the option, "Keep Target", is checked , on the Boolean dialog. ( Unite, Subtract, Intersect)
It's not a Boolean specific issue. All the features which have used "Keep Target" options checked will have the issue.
If the option for 'Keep Target' is checked, the Boolean operation does not act on the original Target body directly, but on a copied one instead.
The copied Target body is an intermediate one, and differs each time during Feature Playback or when the feature is updated.
These alerts can be cleared by hovering the cursor over the feature in the Part Navigator and using MB3 to select "Clear Feature Info Alerts"
Notes and References
Hardware/Software Configuration Platform: all
OS Version: n/a