You can always approach it by going to the Registry Editor. If you aren't familiar with editing the registry, I suggest you back it up first before attempting anything.
You can find the extension at HKEY_CLASSES_ROOT\.yourextension
For example, let's take WinRAR's .RAR extension. For that, I'd have to go to HKEY_CLASSES_ROOT\.rar on the Registry Editor. As you can see on the screenshot below, the (Default) REG_SZ key points to WinRAR.
Now we will go to the registry key that actually contains the application information. That is WinRAR and it should be located on HKEY_CLASSES_ROOT as well. So it will be located under HKEY_CLASSES_ROOT\WinRAR. As you can see on the image below, under the WinRAR key, you can jump directly to shell\open\command.
As shown above, you just edit the (Default) key and place the path to your application inside double quotes then a space and followed by %1 inside double quotes as well. %1 denotes the path to your file.
I hope this somewhat lengthy explanation can serve as a template for you to be able to easily remap your file extension to your newly updated executable. Once you get the hang of this, it should be pretty easy from here-on out.