If I may weigh in, the way the old rdotp value was calculated was a mistake. It was overly optimistic and different from the other dotp values in Skyline ("dotp" and "idotp"), which already switched to NormalizedAngleSqrt() in Skyline v1.4 (from AngleSqrt() in v1.3) in late 2012.
Here is a paper that was the basis for the way we now calculate "dotp" values in Skyline (which are actually "Normalized Spectrum Contrast Angles"):
In 2012, we had recently introduced MS1 filtering (chromatogram extraction) and users were finding AngleSqrt() did not seem to provide sufficiently different values between a highly matching isotope distribution and one that did not match so well. Even before that, the author of the original BiblioSpec paper (https://pubmed.ncbi.nlm.nih.gov/18428681
/), Barbara Frewen, insisted that using the square root normalization was critical to making useful comparisons between spectral intensities.
So, just now realizing that the RatioValue implementation used simply Angle() on the intensities makes it seem even more broken than I had believed.
I did put off making this change for exactly the reason you highlight. People were using the original value, as broken, overoptimistic, and inconsistent as it was from every other place in our code where Skyline professes to have a "dotp" value.
As in 2012, I finally just made the change. Definitely, sorry it has caused you pain, but the old name "rdotp" carried with it assumptions that were not actually true, i.e. that it was the same spectrum comparison function as "dotp" and "idotp".
I hope we can help you recover. You always have the option of simply reporting the version of Skyline you used, and I am sure that version will produce the rdotp values you are reporting.
Thanks for taking the time to post to this support board and share your feedback.