Changing opacity messes up compound paths

[forestj88252896]

Have run into this vexing issue several times, and though it seems to have solved itself before, I'm never sure how. 

Basically, I'm using illustrator to trace over a raster image previously created (image is meant to be a map). This means lots of compound paths and combining or subtracting shapes to create more detailed shapes. Of course, since I'm tracing over something, it makes sense to have the vector layer less than 100% transparent. However, as soon as I put the opacity below 100%, creating a compound path just makes the bottom object disappear. If I do everything as before with 100% opacity, there is no problem. I thought it might have to do with objects being of different opacities, but the same thing happens if I change the new object to the same opacity before applying the compound path.

As I said, I've managed to stumble my way into solving this problem before, but I'm never sure how. Is there a logical explanation for this and how to get around it? Apologies as I'm fairly new to illustrator, and still trying to transfer my raster experience over to vectors.

The base objects at 80% percent opacityNew object, which for some reason is at 100% opacityCreating a compound path (command + 8 ) just makes the base layer disappear...Doing the same thing at 100% opacity works perfectly wellA normal compound path!With all at 100% I can use the pathfinder tool to subtract the object intersections as intended

[forestj88252896 · Accepted solution]

Just an update that selecting "Clear Appearance" in the Appearance box then reapplying the opacity change to the whole layer seemed to fix things (after a great deal of trial and error). Still unsure what was going on in the first place, but I can now create a compound path without destroying everything, which is an improvement.