Old thread, but I'll point out that there is no such thing as "clear anodizing" for aluminum. Anodizing is the process of forming an aluminum oxide layer and then using a dye to color it. Al2O3 forms a layer that seals out oxygen, which it stops the oxidation process and preserves the dyed color.
Anything that is intended to keep the aluminum "shiny" is a clear coat spray of some sort, usually a lacquer, urethane, etc. The only fix if that is damaged (what appears to have happened in the OP) is to strip it all off and reapply.
Ultrasonic cleaner do not attack anodizing nor will it strip a clear coating. You may, however, experience damage to clear coating if it has been damaged by scratching or rubbing through the clear coat as that will give the ultrasonic a corner to work under the clear coating.
Harsh chemicals should not be used in ultrasonic cleaner. Is the cavitation bubbles that do the cleaning, not the chemical. All you need to add to the water is a surfactant to change the surface tension of the water so it will flow over surfaces. A simple soap serves this purpose and you don't need much of it. I use a "vevor" US cleaner for record and a tablespoon of jet dry is more than enough. For my 20L Branson US cleaner that I do things like carburetors in, a tablespoon of something like "Dawn" dish washing soap is all that's needed. The Dawn soap is a surfactant but also deals better than jet dry for holding the petroleum products in suspension once the US cleaner strips them from the parts.
I. personally, just drop my control knobs/levers into a bowl of warm water with some dish washing soap and leave them for a while. Then a wipe and a rinse and they usually come out sparkling clean. It may take a second coat for deeply dirty items. I like to use the least aggressive process possible on face plates and control knows to preserve silk screen lettering and clear coatings.