I run into these loops also, sometimes you want to increase control because it's a good idea, but then get punished for it on your audit because you couldn't implement it perfectly! I'm having the same conversations right not about adding production smocks where there were none before in my facility.
Before you move forward with a final decision, I would encourage you to do these two things first.
1. The 6 lines, is there a risk of cross contamination from tools for allergens, lots, etc? A risk analysis for this project should start here, so that you can ultimately defend whatever practice you decide is best. Sounds like you have this covered by numbering them by line, so good work, but I bet getting employees to comply might be tough.
2. Segregate your hazards/goals into three categories, personnel safety, food safety, and production efficiency. Determine your order of options and preferences in that priority order.
This information will let myself and others on the forum help give you a more specific answer. I'll try to give my opinion based on the information in your post regardless.
how to keep the holders clean in the first place as our knives are segregated by color for both non-food and food contact use
First thing, your product contact and non-product contact knives probably shouldn't have the same or interchangeable holders. With regard to keeping them clean, I can't weigh in on that without knowing if this is a knife block or what. If it's a toolbox or knife block, my response would be simple and that they should get cleaned at whatever interval other DPC surfaces and the knives get cleaned if you're going to use them even with in-use utensils. If don't want to clean the container as often, then knives should only be returned to the holder clean, and should remain on the line if dirty, to be cleaned before returning.
Other than ordering 20 to 30 separate knife holder stations for ease and accessibility for all employees on the line are there any central storage and usage options that don't present a "non-stored" knife issue if an employee needs to keep a knife on a food contact table for the shift?
So a "non-stored" issue is confusing to me. If your production room is active for the shift, there's no food safety reason it couldn't sit on the table like any other DPC surface. In terms of personnel safety, I can understand wanting blades to be put away or sheathed.
Off the top of my head if I was proposing a program for this room, what I might do is have a central location where employees can retrieve clean knives, the location always stays clean and only contains cleaned knives returned from where you do sanitation (nothing goes into the station unless coming in clean). Then for safety/convenience, at each work station, you could install a magnetic block (http://image.made-in...-Knife-Rack.jpg) that's easily cleanable for in-use knives to be stored at the work station. At the end of shift, all dirty knives go to sanitation, get cleaned, and are returned to the central location/stock.
Alternatively, if your lines aren't actually cutting/chopping products and you're just opening bags of ingredients, you could ditch this program entirely and use single-use disposable knives (https://www.google.c...0k1.7GuA0ts_AYA). Selecting colors for dedicated lines or tasks. Do an ROI and see if it's ultimately cheaper to manage.