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Within reason, if you have the wrong focal length entered in PHD2 all that will happen is that your guide stats will be wrong when expressed in arc-seconds. It might calculate an oddball calibration steps figure but if it calibrates properly it will probably guide fine. That ratio it is calculating is your guiding image scale compared to your main image scale, both expressed in arc-seconds per pixel. If you use an OAG you will have that ratio regardless of what you put them on. My ratio is identical when the guide cam is binned 1x1 and both my scopes guide very nicely using that.
It would be worth downloading PHD2 log viewer and seeing what your logs say in terms of the guide star mass and SNR, you might find that as you loose the star you see mass and SNR falling away which could be passing cloud, dewing up of the guide scope etc. This is an example of mine when cloud got in the way. The yellow and white traces are the guide star stats.
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