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Using uVision3 with arm and thumb

I am using the GNU toolchain with uVision3 and my project has a number of files that contain ISRs and must compile in Arm mode. There are other files that can use Thumb mode. If I set the check box for Thumb mode for normal code and clear it for ISR code I can compile as I want. When I click on 'Build Target' the system re-compiles those files originally compiled in Thumb mode as Arm if I compiled the ISR code last or tries to compile the ISR code in Thumb mode if I compiled the Thumb files last. Is there anyway I can stop this?

Thanks
Peter

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