I have had some thoughts and a quick experiment with FTM2014.1 (the MacKiev update). Without some programming, there doesn't appear to be a really easy way to go ahead but there may be a a filtering system available.
By using the "file>export" "selected individuals" option, you can use the "filter in" "all facts" option with "census" "contains" "1881" "date" (or 1841/1911) to select all individuals with the relevant census entries provided you have actual census ("1 CENS") records - FTM should have created these when you entered your census data.
You can now filter out all the registered LostCousins by using the "filter out" "all facts" option, with "LostCousins" " contains" "1881" "date" (or 1841/1911 as appropriate), leaving only those without the LostCousins flag for the selected year (skip this if there are no LostCousins flags, as the entry will not be there to select).
Select OK, then the "GEDCOM" output format drop-down, remove all ticks from boxes, select OK twice and save the file.
Now the messy bit: for each person you enter on lost cousins, you need to add the three lines below before the "1 NAME" line for that person to add the flag (you can do this without creating the LostCousins event in FTM, as it will be automatically created when you merge the first file)
1 EVEN
2 DATE 1881
2 TYPE LostCousins
replacing 1881 as appropriate.
You can delete all the lines after the line starting "1 SEX" to the line starting "0 @", though it would be worth retaining any lines starting "1 FAMS" or "1 FAMC" as these are "family group" links. You definitely want to remove any lines starting "1 CENS" or "1 RESI" or "1 OCCU" and following lines until the next line starting with a number less than 2 to avoid FTM duplicating these records during the merge. You can do this before adding the LC data to ensure it is removed for everyone.
Then you use "file>merge" to load the gedcom data back into the FTM database and create the LostCousins flags.
As always, there is no guarantee this will always work, as it depends on too many factors, so make sure you have a copy/backup of the ".ftm" file BEFORE you merge the data in.
Phil