Here is a fixed copy of your .sky file. You should be able to save this file right next to the .skyd file that you already have and Skyline will be able to open it without error.

There are actually two things that Skyline is having a problem with:
1. In the molecule "NADP" one of the precursors says that it's positive, but the transition under that precursor says it's negative. I imagine that it was a bug in Skyline that allowed that transition to be created in the first place. I fixed it in your file by making both the transition and the precursor be negative (if it was supposed to be positive, I imagine you can delete the precursor and add back the correct one).
2. Skyline seems to have a bug where, if you want to have heavy labeled molecules in your document, you need to associate at least one peptide modification with that label type. In order to work around this bug, I went into:
Settings > Peptide Settings
and told Skyline that your heavy peptides have 13C labeled lysines.

I will try to talk to other people tomorrow and figure out how to get these bugs fixed.
In the meantime, I hope the attached file fixes everything for you.

Thank you!

1. For NADP, its also possible that the transition was changed after I uploaded the transition list. I use the same base skyline file with my imported transitions over time. When I have new results, I just import new results and save as with a new file name, so its possible for that an error was introduced over time (although I don't edit my transitions once they are imported). Looking back on the excel file that I used to import my transitions, the charges match in that. Would it be better to import my transitions each time I create new file?

2. I will use this in the future.

Thank you so much! I really appreciate the help.