I try to describe it in more detail. :)
I have 300,000 SNP genome wide data (ILM HumanHap). And of course I have intensity values and B allele frequency. In principle every kind of value one can export from beadstudio.
For CNV detection I used Log R ratio and B allele frequency and the software PennCNV. This was successful. But because of low SNP density in some regions, you mentioned already, breakpoints are over/ underestimated or a CNV call is completely missing. For special regions I have positive control CNVs which were genotyped via TaqMan/PCR. But I can't call them via PennCNV because there are no SNPs on the array.
In a side project I made a imputation of the 300k SNP data with Impute2. Therefore I used genotype calls (AA, AB and BB).
Now I wonder about a method to use imputed SNP data (genotype calls AA, BB) for calculating CNVs. Over linkage disequilibrium or tag SNP Information or whatever :) I found this, but I'm not sure if it works with my data.