This is a constant frustration as Logic insists on everything being in song form from Bar 1. Really hurts sometimes when scoring or working with film. However there is a solution I think. You can make alternate Signature sets now! Copy the current signature list into an new set to be safe. Make another fresh one and enter your time signatures from the beginning. Then go to the original time signature track and copy that into the new one you just made. This should work beautifully.
8 Core 2.66, 32 Gb ram, OS 10.9.5, L9.1.8 and L10.2.1, UAD Apollo Quad Firewire, UAD-2 PCIE Quad, Interface, Waves Diamond, Melodyne, Antares