Have you tried using Flash Builder Burrito? You can use it with the 4.0.1 Flex SDK to minimize any other changes to your project and/or compiled code. I believe the fix is in there.
Firstly thanks for the quick reply!
Unfortunately, we cannot install the "burrito" preview since we are running into the issue with the installer failing because of our corporate network home drive setup (which we cannot change) :
After further investigation, we found out that we were defining a few of our namespace by referencing directly the packages of our custom component instead of creating a clean namespace as recommended by the flex documentation. Using the package definition works just fine when it is local but our component were located in a swc library.
We were doing this :
instead of generating an xml manifest and basing our namespace on it
We think that flash builder was slowing down because each and every time we were loading up an mxml it had to rescan the said package.