I'm on a Mac Pro using Mojave version 10.14.6
Using Illustrator 2020 & 2021, both updated to latest iterations.

I have a gradient one piece object, I turn a copy of it grayscale through the Edit Color feature > convert to grayscale, I extract the grays generated and ensure global swatches is on to keep swatches linked. Each of this swatch I rename to a specific designation. I used this grayscale gradient and use it as an opacity mask, this serves as a density mask that allows me to control the opacity of each section of the color gradient separately.
Now I duplicate this art along with opacity mask as a new layer, I drag it to new layer to duplicate it. This new art will serve as an alternate density control with different opacity values for each color, I want to rename the existing gray swatches but i want to keep the old values too at this point both share the same gray swatches with one set of specific designation. So I go into the original gradient art opacity mask and "cut" the gray converted art into the clipboard, keeping it safe. I then proceed to rename the gray swatches to the new designation and adjusting the gray values through the K slider after that is complete I re-paste in place the data in the clipboard back to where I cut it from. The old gray swatches reappear in the swatch table, however here is where the bug occurs. When i click on select unused swatches to check for linkages the swatches that returned from me repasting back the grayed art into the opacity channel is now unlinked and for some odd reason returned grayed gradient art which should have been insulated in the clipboard is now using the new renamed swatches from the new duplicate.

The new swatch sets and the old swatch sets were supposed to maintain links to its respective gradient art.

So far this happens to gradients converted to grayscale 80% of the time, I think this is a bug as 20 percent of the time functions as it should like with other objects with single simple swatches.

My background is color separation for t-shirts and i use this method to generate grayscale underbase plates that allows me control of the color density in each color area.

Hoping for a fix for this, thanks,
Homer Bobis