Did you ever figure this out? I am having exactly the same issue!
Thanks for bringing this up.
We have filed a bug for the same:
The bug is under investigation and please refer to the bug report for any updates.
From the bug:
Flash Builder currently ignores linked folders while copying resources if their actual location sits outside known source containers.
A simple workaround would be to create a new source folder (this is a link as well and can point to an existing folder) via Project Properties -> Flex Build Path that contains the files that need to be copied to bin-debug/bin-release.
Would this work in your case?