If at any point physics warp is activated then after the game is not able to make many useful calculations.
No more maneuver nodes (the dV of the node is constantly going up at about 25 m/s/s), no more navball marker reliance (those dance all over the place) and no more rendezvous planning (when you make encounter at low Kerbin orbit by the time you get there target will be several hundred km away).
The only way to restore ability to use those features is to completely restart the game. Going back to main menu and reloading the save does not work.
2.3.10.1 with 1.4.5+exp