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Were homozygous reference SNPs removed?
Yes... however I am dealing with a haploid organism and I want all SNPs to be included. IS there a way in which I can do this?
If it's homozygous to the reference, does not mean that by definition, it isn't a SNP?
This post may be helpful.
How To Convert Vcf File To Plink Ped Format?
especially the answer in the end.
One possibility could be that some SNPs fail the MAF filter. You can also make the conversion using plink 1.9 plink --vcf vcf_name --make-bed --out name (https://www.cog-genomics.org/plink2/data) this will give you files in the plink bed format.