We had bad light when rinsing last night and today the grout seems uneven in the lines. If I mix grout tonight can I fill in some of the problem areas? Or do I have to dig out all the grout first?
If you want to be sure, yes, you have to dig all the grout out first. Grout bonds mostly to the tiles, less so to itself. If you dig the grout out, try to do it at a 90 degree angle to the "proper height" grout, this will give you the best adhesion for your patch. Also, if possible try to make those 90 degree joins where there's more tile to adhere to (avoid starting a new grout line at the corners).
However 48 hours is right on the cusp of where I might try to fill it in. Typically grout takes a few weeks to fully cure, but is ready to seal after 2 or 3 days. That says to me that you might still get the new grout to bond to the old. I know there are cases where a homeowner might accidentally scratch the grout, in general, the tile mechanic doesn't always scrape up all the grout, before fixing something like that.
Keep in mind, if the new grout fails, it will be harder to dig everything out later than now. The grout is softer now, all the materials are at hand, and there's incentive to finish the job.