Half of my variants get rejected by using picard LiftoverVcf

Hi,
I want to include samples which are aligned on b37 and hg19 for genotypeGVCFs and VQSR with b37. I have used picard LiftoverVCF on gvcf files with hg19tob37.chain. But 60% of variants are rejected due to mismatching reference alleles. In this scenario should I realign the samples on b37 ? .Please give some suggestions on this regard.