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There was some uncertainty about the role the number plays in data cohesiveness. Personally, I feel it's the glue that holds everything together. When we speak about atomization, I think it's the phone number that binds those atoms into a critical mass. I'm not debating the merits of pay-per-call, but I am interested in hear from those in the know -- is not the phone number the common thread that holds the tapestry together?
Obviously, other matching criteria can be used as well, such as street address, but there are situations where phone number will be used/trusted more such as for businesses in malls or shopping centers or in big office buildings -- all of which have many businesses sharing the same street addresses.
So, using special tracking numbers mostly impacts the abilities of directory sites to properly aggregate your data with their various data sources.
I don't really think it would hurt traffic to your online biz information, nor overall referrals to your business.