I just received an e-mail of someone wondering whether Sigasi HDT can preserve whitespace and comments when VHDL code is refactored:

When you apply a refactoring, some code will be rewritten. We do this by first calculating the minimal set of changes needed for the refactoring, and then applying them. This way we make as little changes as possible, preserving the original text where possible. As a consequence all comments should be preserved.

You could of course also try it for yourself by downloading the trial