Sorry, but I really can't "square" the comment that you reference with the general prohibition against ex post facto laws, and apparently, neither can Militarybook (which gives me some measure of comfort). It may be that there is some particular point of patent law that applies and that we are unable to comment on because it's outside our fields, or, alternatively, the comment may simply be a "cya" provision that didn't really need to be quite so broad.
Generally speaking, and as I have posted before though quite some time ago, laws that are substantive in nature cannot affect situations or agreements that are already in existence. Otherwise, there could never be any certainty in most of the relationships in everyday life --- for example, that bazillion-dollar contract that a company was able to negotiate last year, and which is expected to bring in ongoing revenues for the next 10 years, could be taken away with the swipe of some legislator's pen at any time during that 10-year term. Society simply could not function in the face of such legal uncertainty.
On the other hand, non-procedural laws, commonly referred to as "procedural" in nature, are often considered retroactive. These laws don't affect the "substance" of anything, merely the means of getting there. Even such procedural laws, however, cannot adversely affect a right that has already "vested".
Thus, even if there are provisions in the Patent Reform Act that, for example, might be directed toward curtailing the types or extent of damages that are recoverable in the future, and even if those provisions could be considered "procedural" rather than "substantive" (which I wouldn't be able to understand in the first place), they still couldn't affect the right to recover such damages under patents that were already in effect. Conversely, a provision that would merely limit the available venues where a lawsuit could be filed (which might, for example, exclude Marshall, Texas as a venue for PTSC) would probably not be prohibited --- I don't know whether the Act contains such a provision or not, and I am just using giving an example.
I know all of this is probably pretty confusing, but libraries could be filled with the scholarly discussions that have been published in the area of "retroactivity of laws". As such, there is simply no clear answer, unless some patent lawyer out there is lurking who can be of assistance to us.
Best wishes.
