Hi, we have changed the default values in the links.def file for Contact Name, Contact Email, so that when we input a record internally we don't have to keep retyping those two fields.
Will this cause a problem when someone else adds a new record from the regular addition field?

It shouldn't matter. The add.cgi uses a different form than the one used in the admin screens. If the <input> tags for those fields contain a value="" (to ensure they are initialized as blank) you should have no problem. That is, as long as the %add_system_fields variable in links.def does not include the defaults for Contact Name and Contact Email. If those are included in %add_system_fields, then they will always be added to a new record no matter what.