This is the better solution I found for this, using Photoshop and QGIS only.
Open tiff file in photoshop and paint pixels. Depending on what you want to edit you may paint either black or white pixels (black pixels are masked out - no values, and white pixels have values). Save tiff file as a copy (avoid to overwrite the original file).
Open QGIS, use the georefencer tool in the Raster menu, import the edited tiff file and import 'GCP Points' file with the respective coordinates. The GCP file should have the same name as the edited tiff plus the extension .points (example: fileName.tif.points). The contents of this file should look like this:
Every row is a corner point in the image. From top to bottom the order of my points is: upper left, upper right, lower left, lower right. The first two columns are the extent coordinates obtained from the metadata of the original tiff (you can get it from the raster properties using QGIS). The next two columns are the extent of the edited tiff (the width and height in pixels). Note that the extent of my image in width (x-axis/longitude) is from 0 to 12879, and the height (y-axis/latitude) is from 0 to -11183. The signs are important. The other column values can be 1,0,0,0.
So you can georefence your image by loading this file in the georefencer tool.
- Finally I used this edited tiff file and used it as a mask to correct my original raster. The output looks like this (blue-corrected image and red-original image):