You can easily complete the process in one go when you are using the reliable tool. The better way is to collect all files in one folder, keep a backup and then scan them together.
For this process I choose the Softaken vCard Duplicate Remover, which can load single or multiple vCard files and find repeated contact entries in bulk. It can check common fields like name, email address, and mobile number without sending your contact list to any online server. After cleanup, the new VCF file can be saved in your folder.
Test the free demo; that gives you a clear idea.