Differences between V1 and V2

[smerella]

Dear Developers,
In our lab we introduce DECoN to identify putative CNV for samples enriched and sequenced with illumina TruSight Cancer kit.
Recently we installed in our server, the V2 and yesterday I tried the new version in previously analysed runs.
Surprisingly, I obtained different results, despite the fact that genome version and bed used are the same.
Can you please describe me the differences between the two version?
Are there tests that I can perform in order to evaluate which results are more reliable?
Moreover, the documentation has an error: is indicated the option --Rdata while the correct one is --RData.

Thanks in advance,