First, let me say that the counties in question have come up with a plan that they can live with, so this discussion is proceeding for information purposes only.
I do not know about other states, but in Florida people can be a legal resident of a county without having a specific address in the county. In most cases, these people are listed as living at the courthouse. The main example of this is military personnel and their families living overseas. They do not have a house in a county, but they choose a county of permanent residence. Note that all of these people always vote by absentee ballot. (Military overseas people frequently choose Florida as their state of residence since Florida has no state income tax.)
Since they do not have a real residence in the county, they do not live in any real precinct on the map. Some counties choose to place these voters as residing in the courthouse in a special courthouse absentee precinct. If this type of report precinct is created in GEMS, a line on the SOVC report results. Note that since the person in question does not live in any specific place in the county, they typically do not qualify to vote in any single member district races in the county, just the county wide races.
If the county does not use precinct Id #s on their ballots, and the county does not want zero votes to appear on the report for said report precinct, they need to separate these absentee ballots out from the rest of the absentees and then feed them through the memory card for that report precinct. If they do not want to go through the process of separating out the absentees from the permanent absentee voters, the results only show up in the general absentee totals, and the special precinct shows zero votes.
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Mark: I am not aware of anyone counting voters in anything other than the precinct of which they are a resident. I am not sure what they are trying to accomplish. They can get a report reflecting absentee voting. If the voter is not listed in a report precinct how will they determine the ballot they are to receive. It would appear they are wanting the person in 2 places.