We had something come up over some of the older CCD data having bad columns in it and so I will show how that will not be a problem if you use the right settings in Astro Pixel Processor. The built in calibration it has will make them go away. For this I am using the AUS-2-CCD M6 data since that was mentioned.
First, go ahead and load up your data. I went ahead and used all of the M6 AUS-2-CCD data for this, because why not? One of the cool things in APP is if you are using the already calibrated data from Telescope Live you can simply load every light on the object at once and not worry about picking what filter it is, and because of normalization and LNC (tabs 5 and 6) you generally don't even have to worry about specifying a session. There are a total of 120 lights taken as a couple different sets, but both are roughly centered on M6, so I am using them all since it gives a 20 hour integration.
Here is where the magic happens with getting rid of those hot and cold columns that show up as a line through the image. Go to tab 2, scroll on down some, and when you see the Cosmetic Correction spot go ahead and check all 3 things for cosmetic correction. When using CMOS data you will only do the hot pixel one, or if you have CCD data and no bad columns in it then you will also only check the hot pixel one.
On the cold column kappa and hot column kappa when you hover over the values it will state that a kappa of 3.0 should correct almost all columns, and lower than may correct columns that do not need correction the default values at first since that would tend to work on most things. I have had good luck depending on the image with anything from the default value down to 4.5 or so and have not needed to go lower. For the purposes of this I set them at a kappa of 5.0.
Now all you should have to do is make sure you have the rest of your tabs set where you want them and simply hit integrate. On tab 6 Integrate I will set it to 2nd degree LNC and enable MBB at 10%. I pretty well leave the rest of the tabs at their default unless I need dynamic distortion correction, which is set on tab 4 Register.
Now we have a final result when these are combined that shows no bad columns left! This is not the final product, just the initial RGB combine, but you can see there is definitely a file to process out and work with here.