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The P-51 is probably the only module that needs to be done separately from the rest, because it has localization. In other words, there are different aircraft folders depending on where you live. Apparently the US version is different from the rest of the world, or something like that. I’ve never been able to solve this.
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I usually use Merge and Overwrite Existing Binds command so that I don’t lose the inputs that I haven’t programmed in JoyPro yet.
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Occasionally, you will blast out your profile, start DCS, and nothing is programed. Usually restarting DCS works to resolve this, or send them again (always with DCS shut down), and they will be there. Make sure that your DCS instance is correct on the bottom dialog box before sending. I’ve never had to rebuild completely from scratch.
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You did backup your \Saved Games\Config\Input folder as I mentioned in the OP? If so, just copy it back to the original path to retore your original controller profiles.
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The best place to get support, is to post in the author’s Discord server in the issues-bugs or questions section. He is pretty good about replying.
JoystickProfiler for DCS