In Skyline, you should go to:
Settings > Transition Settings > Filter
and change "Ion Types" to "f, p".
Currently, you have that set to just "f", which makes Skyline think that you do not want any precursors in your document. Because of this, if you make any change to your Transition Full Scan settings, such as choosing a different mass analyzer, Skyline wants to make sure that all of the transitions in your document agree with your settings.
I believe earlier versions of Skyline did not do this sort of stuff for small molecules, but the current version of Skyline thinks it needs to delete all your precursors because they do not match the specified Transition Settings Filter.
By the way, if you encounter other situations where you have all of your transitions the way you want them, but Skyline keeps trying to change things, you might want to uncheck the "Auto select all matching transitions" checkbox at "Settings > Transition Settings > Filter".