I had to manually update the TSV files where this data is being appended. So, every night a cron runs and computes the new numbers for the previous day. It runs each SQL script and appends the results to the corresponding file found at: stat1003:/a/limn-public-data/language/datafiles/<<corresponding-file>>.tsv
So, when the SQL was changed, the TSV no longer fit the new rows which had two additional columns. The fix is manual but simple, just add the new columns to the header row in each file, in the correct order (same order as the SQL file). I've done this for the existing files and (after the files rsync-ed over to stat1001) you can now see minwiki and uzwiki in your graphs: http://language-reportcard.wmflabs.org/
In the future, to make these header row changes yourself, you'll need access to stat1003, and access to edit files owned by the stats user. I think @Nikerabbit's gonna ping you guys tomorrow about these rights. Remember to change the file after you merge the SQL changes. It won't break anything if you don't but the graph would have two empty columns until everything's on the same "page".