It was Allen Edmonds saddle soap, and I did indeed use water. I'm not completely against saddle soap, but I think it should be saved for more extreme needs.
While I'm certainly not a chemist, I don't think it was the ph change that did it....moreso the abrasive qualities. It was no longer shiny/smooth like the rest of the leather, but was instead matte and more porous.
For reference, here's the boots I'm referring to, directly after I had saddle soaped and then applied obenaufs. I've obenaufed other Beckmans and had zero issues.
Wow, that is quite a drastic effect. I am quite suprised that you had such a result... makes me think twice about using saddle soap myself.