There is a previous biostars post that deals with the use of plink2's --split-x flag to handle cases when a large number of markers need to be moved to XY (https://www.biostars.org/p/98211/), or chr25 in plink coding.

However, my case is a bit different.

Although the data that came from the sequencing center already appears to have a chr25, I am still getting the error:

180461 heterozygous haploid genotypes; set to missing
Writing list of heterozygous haploid genotypes to [ file.hh ]
44121 SNPs with no founder genotypes observed

However, running plink2 gives:

4221792 variants and 191 people pass filters and QC.
Among remaining phenotypes, 191 are cases and 0 are controls.
Error: --split-x cannot be used when the dataset already contains an XY region.

So, I did a little digging and I found that nearly all of the SNPs that end up in the .hh file are on either chrX, chrY, chrXY, or chrM (corresponding to plink chr23-26).

Further, it seems that although many are at the beginning and end of chrX, others are in discrete regions, and some are on chr24 (Y) or chr26 (M), and there are a few others as well.

I am wondering now what my next steps should be or what the options for next steps are and why. Thank you very much for your help.