I see that the default value for the PureCN.R --maxhomozygousloss option is 0.05,1e+07.  Does this mean that if entire chromosome arms are lost, they must not total more than 5% of the genome?  

It means that homozygous losses are not accepted in the optimization when the corresponding segment is larger than 10Mb or when more than 5% of a chromosome (whole chromosome, not arm) is completely lost. This is mainly to avoid wrong solutions where a complete chromosome is assigned to a homozygous loss state.

The default is calibrated for medium sized panels. With small panels, MTAP/CDKN2A deletions might exceed this cutoff if you have only few other genes surrounding them and you might want to increase. Future versions might be a bit smarter here, see https://github.com/lima1/PureCN/issues/50.