But the earlier beds have sunk about 3". Do I need to dig up the perennials and shrubs to put in more soil under them? Or can I just add more soil gradually to the plants and expect their roots to push them up to the optimal level? (I read once somewhere that lily bulb roots push or pull the bulb to the level where it's happiest.)

The reason I don't see this question as self-evident is in wondering about shrubs and trees in forests. We live in the PNW, and there is certainly a heavy layer of needles, arbutus leaves, etc that blanket the soil every year, and wild plants don't seem to rot at the crowns.

I'm not trying to avoid the work, just the possible stress to plant roots and plants. Any thoughts are most appreciated, and thanks in advance!

In your case, you added a lot more organic matter at once, and dug or tilled and mixed things up. This has the effect of fluffing the soil with air. It will settle a bit over time. In addition, the compost you add will continue to decompose. Only the mineral portion of soil will be permanent. It's fairly common for this to happen with new raised beds, and the effect is worse the more organic matter you used.

I know there's another thread on this just in the last week or two, I'll try to find it.

I would be more concerned about woody plants than bulbs and perennial flowers etc. which die back to the ground each year and can generally adapt to an inch or two of new soil (if they aren't highly sensitive species).

I would add soil slowly around woody plants, not more than an inch a year, but that's total guesswork on my part.

Also, cut down the organic content of what you add and use a higher mineral fraction so it will stick around.

I am still wondering, though, from a quasi-scientific perspective, whether there is, in fact, any ability or inclination of roots to manipulate plants to an appropriate level.

(Since I've been marvelling at various aspects of "intelligent design" in my garden over these last years, I was also musing if they had intelligent roots.) :)