Large VCF files usually get duplicate contacts when you export or sync data multiple times. Removing them manually is risky because similar entries may still have different numbers or emails, and one wrong delete can cause data loss.
The best approach is to keep a backup first, then use a duplicate cleaning method that scans the whole file and identifies repeated contacts automatically instead of checking each entry one by one.
WholeClear vCard Duplicate Remover is the solution that can be applied here for removing duplicates from bulk VCF files without having any effect on original contact information.
After cleaning, just re-import the file and check a few contacts to confirm everything looks correct.