The solution to this, is to finish your sprites at very large resolutions, and optimally all lineart and color should be completely digital. This is of course limited by your computer's RAM. However going as large as you can while maintaining proper speed with enough layers for all your colors is a necessity.
For sprites and most line art based images, I use SAI.
Whether you start the sketch traditionally, or digitally, it is important that at your linework is high enough quality at the highest resolution you can manage.
For example, to facilitate any resolution that might be necessary, all sprites that I have done have started at 5000x tall like Aunyrae. In Sai this resolution gives me good flexibility in how many layers I have with only 4gb of Ram (most production artists for VNs work much, much higher, sometimes twice as big, with 16gb of ram+) I consider 4gb of Ram to be the normal, given how extremely cheap Ram is today, you should have similiar capabilities to me. But this is still very ram intensive, and it's advised you do not have a browser open while drawing.
An example of two characters, both sketch form and lineart form.
Line art is a stage that is quite difficult at this resolution. It's important that your lineart is done entirely on it's own transparent layer, and when finished it's important to lock the transparency of the layer. Accidents in coloring the wrong layer might ruin your lines!
It requires practice and a lot of scrutiny. Removing gaps and frayed lines, or avoiding them all together. This is very time intensive, and for many people it is the most crucial part of the image, as bad or wavy lines can unbalance a picture. Another reason why you must make sure your sketch has been so scrutinized at this point. Is because, once your line art is done it is very difficult to change the pose without redrawing almost everything.
The tightness of the lines makes it so that cropping lines out, re-scaling, or rotating them will ruin the lines. At this point it is very difficult to re-salvage those lines. If it's a large part of your image, you're better off re-doing that entire section.
90% of all effort will be in the initial design, sketching, resketching, lineart, color, etc. than any other part of the sprite set.
At this point you will have a very large sprite master which you can resize at will to test any resolution you could want. What is a large amount of front-loaded effort in design. Has saved you or your team massive headaches. Because you can re-scale the sprites around the game. Not having to re-scale the game to suit low res sprites.
I hope this has been helpful for people who are looking to do sprites. I admit my artwork is not perfect, but I believe this gives a lot of examples of the stages in sprite creation. As well as giving you an idea for saving yourself lots of headaches in the future by taking on one big one at the beginning.