I was just tackling a similar problem. A few SNPs in my .bim file were present in duplicates, triplets or quadruplets (PLINK recognises all as duplicate variants). Firsly, you can recognise which are the problematic positions using PLINK 1.9 functionality --list-duplicate-vars. Secondly, to keep one copy and remove subsequent repetitions we need to use PLINK2 functionality: --rm-dup force-first

Worked like a charm for me.

plink2 --bfile inputfile --rm-dup force-first --make-bed --out file_cleaned_data