uspto.gov publish statistics quarterly, but the numbers are averaged from all industries and fields. I am trying to figure out whats chances a software patent had in 2011/2012 to go through a ex parte reexamination and come out with all its claims intact. Looking at reexamination certificates issued for 2011/09/30 -> 2012/09/30 as published by USPTO, I can see that about 12% of the certifications had all their claimed confirmed during that time frame, however, is that number the same for software patents specifically?
One big problem with such a question is that there is no such thing as "software patents". Software itself is not patentable, it is what the software does or is used to do -- the method -- that is patented. Software may be used to implement the whole invention (many data processing patents) or only one component of the invention (e.g. Diehr.) Many would not even consider Diehr to be a software patent, despite it being considered part of the "patent eligibility trilogy".
There are a number of categories and sub-categories ("art units") that patents are classified as, and you could try to carve out "software patents" based on some of the relevant categories, but that is still not going to be a very rough way of doing so. This is because art units are organized based on the field the invention relates to, rather than how the invention is implemented. Software simply happens to be how inventions could be implemented. As a very inaccurate example, a "security/authentication" art unit could encompass software methods such as the RSA algorithm as well as hardware solutions such as RSA tokens.
As an aside, one of the biggest shortcomings of many early research papers that try to analyze software patents (especially from authors such as Bessen, etc.) is that they are based on very inaccurate classification methods, such as PTO and EPO classifications. As such any conclusions are far from reliable.
So you can guess why the PTO won't even attempt to try to provide such statistics for "software patents": nobody, least of all the Supreme Court, seems to be able to concretely define what a non-abstract software patent is.
It's not that simple. The statistics only account for three situations.
All clams lost.
No claims lost.
At least one claim amended.
There are no statistics for at least one claim surviving,but in my experience it would be about 50%. Software claims don't get any special treatment.
Not a direct answer, but the former head of the USPTO gave a comprehensive speech about the state of examination of software patents late last year. It does touch on reexam. Dave Kappos on Software patent examination