I am using Eage to phase plink input. I maintain --keep-allele-order throughout my workflow. Eagle outputs  .haps (Oxford phased haplotype file), which I convert to VCF with shapeit. I did some sanity checks and find that this process reverses REF/ALT designation and genotypes  for every single one of my snps and indels. Comparing alt allele frequency to reference  strongly suggests that I do not have a build issue, so the workaround was initially to do 

`bcftools norm --check-ref -s -f hg19.fa input.vcf > output.vcf`

to flip everything back after converting to vcf with shapeit, which perfectly flips every single one of my snps, but does not seem to do the same for indels. Is there a way to do this for indels as well. My alternative thought is just to use bcf as input for eagle, which should avoid the Plink/Oxford formats completely. 
You should be using plink 2.0 instead of 1.9 as much as possible whenever allele order matters.  Otherwise, if you forget --keep-allele-order even once, you're in trouble; and there are some plink 1.9 commands (like --linear/--logistic with interaction terms) which need to NOT be run with --keep-allele-order.

You can use plink2 [--ref-allele][1] to reset the REF alleles in the manner you want; see in particular the second bullet point in the documentation.

And as for *every* variant having REF/ALT reversed, that sounds like you did not import the initial file correctly.  Recent plink 2.0 builds make that particular mistake a lot less likely by forcing you to declare whether an Oxford-format file has REF first or last.

  [1]: https://www.cog-genomics.org/plink/2.0/data#ref_allele