This doesn't necessarily mean the original holding was wrong--remember that probably *most* software patents have become invalid in the last fifteen years.
Most are never challenged, but you are right that those few which get challenged are frequently invalidated.
I've learned from various discussions with my legal department friends there are many changes in patent agreements over the past few years.
(Liberally using "we" and "you" to represent the sides:)
* Indemnity rules are slightly changing. If we are licensing your patents, if someone else comes after us about your patent, companies are making it more likely you pay the costs.
* Payment is more often gradual over time rather than once-off. Patent rules don't allow for 'refunds' after using a patent. (Mostly to stop someone for using a patent for many years, then after getting enormous benefit, challenge the patent and try to get a refund.) But they do allow payments to be held in escrow for a short time, allow temporary holding of payments during a challenge, and allow termination of payment if the patent is invalid or unenforceable. To hedge the bet they may pay a little more money for the patent license but spread it over the full duration, or make payment based on milestones hit (such as getting a successful clinical trial, or having the product available in stores, or reaching a financial threshold), or making balloon-style payment with moderate size payments over time plus a large final payment.
* Licensees are making explicit the existing requirement for repayment in events of fraud or material misrepresentation, including if the fraud was against the patent office. This makes it a little easier to enforce one of the rare ways to get money back from a bad patent license.
* Licensees are focusing more on the description of use rather than the patent numbers. This helps in cases where there may be several closely related patents. Already the courts have ruled that you cannot add new patents that block us from using a patent we already licensed. But this protection is that if we licensed specific patent numbers with the intent to do a certain thing, and you have other patents related to doing that thing, the license covers those too.
So yes, businesses are adapting to a world with an increasing number of patent invalidation and certain troll tactics.