When you are creating a spectral library from peptide search results, including Proteome Discoverer, you can specify a cutoff score.
PSMs which did not score as well as that cutoff score will not be included in the .blib file that is created.
That is the usual reason that the .blib file will have fewer entries than the original peptide search results.
For PD, I believe that if you specify a cutoff score of 1, no filtering will be performed and the .blib file will contain all of the entries from the .pdresult file.
For other types of search results, the cutoff score that corresponds to no filtering is 0.

Checking the "include ambiguous matches" checkbox will sometimes result in more entries in the .blib, but I believe Skyline always gives you a warning when ambiguous matches end up being excluded. That is, during the process of building the library, Skyline will show a message saying "The library built successfully. Spectra matching the following peptides had multiple ambiguous peptide matches and were excluded:".
If you did not see a message like that, then there were no ambiguous matches so that checkbox won't make a difference.
-- Nick

Thank you very much! For PD, the score means percolator q-value, which indicates the peptide(or PSM I guess) FDR. I believe this threshold is necessary for me, as the peptides filtered out are not unreliable.