Yes, this can be done quite easily, but it requires multiple 'find and replace' operations using a 'plain text' editor.
The shortcut file itself is just an .xml with different extensions for win and mac - respectively .wfx and .mfx
I am a windows user myself, so can't give recommendation on 'plain text' editors for mac, but there should be plenty of options.
I have written a few articles on Flash shortcuts which explain how the shortcuts files are structured and what are the differences between the win and mac versions - flags, scope, etc.
Read the articles to get familiar with the file before starting to change it.
1. Keep a the original .wfx file if you need to repeat the operation. Create a duplicate and change the extension to .mfx
2. Open the .mfx file in a plain text editor
3. In CS6 you don't need to worry about the 'scope' values - they are all the same across win and mac
Do as many search and replace text operations for the 'flags' values as you need to get them all changed to mac format, using the 'flags' table in
Basically this means that if on windows you have a line such as:
<Shortcut id="33580" key="49" scope="IDR_MAINFRAME" flags="11" />
on the mac it has to become:
<Shortcut id="33580" key="49" scope="IDR_MAINFRAME" flags="17" />
So you search for flags="11" and replace it with flags="17"
As you will see in our table you may have different values for win which mean the same thing (8, 9, 10, 11) - all of them should become 17 for the mac shortcuts.
4. When all is done, save your file, start Flash and test. If something is broken, you have missed something. Close Flash and look again.
It's a little intimidating at first, but then you learn.
My advice is to try with only a small file with only a couple of shortcuts at first.