Filter max-missing multiple time removes more SNPs

Question

[QPaps04]

Please can someone explain to me why this happens?

Here are the steps I take

1. I carry out a filter on max missing using:

   vcftools --vcf filename.vcf --max-missing 0.8 --recode --recode-INFO-all --out miss_80

2. I then thin the vcf by using:

   vcftools --vcf miss_80.recode.vcf --thin 250 --recode --recode-INFO-all --out miss_80_thin

This vcf has 2,573 SNPs in.

1. I then filtered again on -max-missing (as I am still having issues with PCA analysis) at 80% using:

   vcftools --vcf miss_80_thin.recode.vcf --max-missing 0.8 --recode --recode-INFO-all --out redo_miss

This has further reduced the SNPs to 1,462

What I dont understand is: If I have already filtered for a missingness of 80% why do I still remove SNPs when I filter for the exact same proportion the second time around? Surely all the snps that have higher than 80% missingess have already been removed?!

Sorry if this is a basic question - I cant seem to get my head around what exactly is happening here. Thank you for your advice in advance! Happy Holidays to all :)