Hello folks,

I also run into the same issue as you guys (Atik 314+, Atik FW2, kstars 3.5.8 on astroberry 2.0.4). I would also be pleased to have a fix for this issue.
Nevertheless, I wrote and use a python script as a workaround. It adds the FITS filter value in the header based on the file name writen by Ekos. I run this script on my astroberry after each session before downloading the files on my PC.
Hereafter is the code. You may want to modify the base directory path (base_dir) and the filters name for your particular case. Of course, the filter name must be present in the file name.
This works fine for me. Please, make some tests before on some copy of your files.

"""This python script fixes the FITS filter information based on the fits file
name. One need to install astropy python module before running
this script.
"""
from astropy.io import fits
from astropy.utils.data import get_pkg_data_filename
import os

#All the fits file inside this directory will be checked and fixed if needed
base_dir = "/home/astroberry/Pictures/Astronomy"

for root, dirs, files in os.walk(base_dir, topdown=False):
    for name in files:
        if os.path.join(root, name).endswith("fits"):
            #print(os.path.join(root, name))
            fits_file = os.path.join(root, name)
            d = dict(fits.getheader(fits_file))
            #print(d)
            # if the FILTER attribute is not present iht the header...
            if not "FILTER" in d:
                if 'Red' in name:
                    print("set Red for {}".format(name))
                    fits.setval(fits_file, 'FILTER', value='Red')
                elif 'Green' in name:
                    print("set Green for {}".format(name))
                    fits.setval(fits_file, 'FILTER', value='Green')
                elif 'Blue' in name:
                    print("set Blue for {}".format(name))
                    fits.setval(fits_file, 'FILTER', value='Blue')
                elif 'Luminance' in name:
                     print("set Luminance for {}".format(name))
                     fits.setval(fits_file, 'FILTER', value='Luminance')
                elif '_Ha_' in name:
                     print("set Ha for {}".format(name))
                     fits.setval(fits_file, 'FILTER', value='Ha')
                elif '_OIII_' in name:
                     print("set OIII for {}".format(name))
                     fits.setval(fits_file, 'FILTER', value='OIII')
                elif '_SII_' in name:
                     print("set SII for {}".format(name))
                     fits.setval(fits_file, 'FILTER', value='SII')
                else:
                    print("No changes in {}".format(name))

Cheers,
Sebastien

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