Similar to Neil's suggestion, you can actually just save a CSV file in your sync folder but without adding any values. This will also allow you to permanently set the order of columns in your resulting CSV and spreadsheet.
Just add all the column headers, comma-separated, into the first line and create a line break, but keep the second line empty. (You'll have to do this in notepad or similar program.) Then just save it in the sync folder under the same name the CSV would normally have. KoBoSync/Form will then just append the new records starting with row 2, but keeping both the order intact and leaving all variables as separate columns. Just remember to create a line break at the end of the first line.
For example, your csv file should look like this:
[line 1] instance,deviceid,key,start,end,A01,A02,A03,...
[line 2]
As an example I'm attaching a file that does that.
The thing I usually do is create a fake record in which I select all possible answers. When aggregated to CSV, you get a file with fields for all options. You can delete the fake record, and leave the CSV shell. The next time you aggregate real data, as long as the folder settings are the same for where the CSV is stored, it will write the new data into the old CSV, and there will be columns for every variable, even if those variables are NULL.
~Neil