The clear layer at top will continue to work for etching. The bottom layer, I suspect, is the same solution as the top layer, but contains suspended particles ("mud"). The mud is a mixture of iron and copper oxides and chlorides. If you take a little bit of the mud, add some HCl and bubble air through it, it will probably redissolve and give you a greenish-brown solution containing copper(II)chloride (cupric chloride) and ferric chloride.
In other words, if you start with a ferric chloride etching solution and use it only to etch copper, it will last forever, if you replenish the chloride using HCl and keep it oxidized. Eventually, it will become mostly cupric chloride, which is a deep emerald green color. Cupric chloride is a good etchant in its own right. The amount of acid you need to add can be determined by titration -- something like 1 molar free acid should work -- or just by experience. Too much acid will cause more undercutting during etching. If it etches too slowly, adding more acid will speed it up.
If you have 100 mL of solution + mud, I would add 10 to 20 mL of concentrated HCl, then bubble air through it overnight and see what happens.*
The solution becomes more viscous with the mud. Your choice is between adding HCl and reoxidizing the bath versus just filtering off the mud. A little mud doesn't hurt the etching, but if the solution is too viscous, it will slow down the process, make getting fine lines more difficult, and make observation more difficult.
John
*Concentrated HCl, 38%, is about 12 molar. 10 mL diluted to 110 mL total volume = 1.1 molar in the final solution.