I had this error when I tried to merge two binary files with plink 1.07.
Warning: different physical position for rs3926405
Warning: different physical position for rs365066
Found 58757 SNPs that do not match in terms of allele codes
Might include strand flips, although flipped A/T and C/G SNPs will be undetected)
Writing problem SNPs to [ AfricaKhoisangeno0.05hwe0.001Batwakiga.missnp ]
ERROR: Stopping due to mis-matching SNPs -- check +/- strand?
and it worked but in the case that there is many more error about SNPs physical position, what should I do? I do not want to loose too many SNPs data as I did before.