From user who experienced Hangouts issue in screenshot: clicking does indeed bring the icon back.

I would guess one of two things here:

(1) In the screenshot it looks like the missing icon is the rightmost thing on a horizontal shelf. I wonder what would happen if the Files.app icon were moved to a different shelf position. Does the Files.app icon still disappear? and/or does the new rightmost icon ever disappear? +ludomagno@, do you mind trying this to see what happens? +mohsen@ also.

(1.5) How about with a different shelf orientation?

(2) This could be a bug specific to the Files.app icon and unrelated to the shelf. +fukino@.

Right now my money's on (2).

I cannot reproduce the issue unfortunately, will try the suggestions in #2 as soon as I'm able to.

It happens with both Files.app (for me) and Hangouts (in screenshot), so if it's due to the icon it isn't specific to Files.app.

I believe I've seen it before when Files.app wasn't the last item in the shelf (I seem to remember noticing a gap), but I can't be certain. It could have been my last-pinned app though.

Marking this as up for grabs and removing the MD label.

tbuckley@, are you still seeing this? It's possible my earlier shelf work was at fault.
This area has undergone some more recent changes, so it may already be fixed on 63.
(After crrev.com/c/692749 shelf icons are sent from Chrome->Ash via Mojo IPC)
(crrev.com/c/699417 fixed high-dpi and crrev.com/c/705269 addressed efficiency)

I haven't seen it in quite a while, so happy to close it and re-open if it pops back up (I've been dogfooding Eve which a pretty atypical Chromebook).

I do hope it was fixed, please reopen if you see this again.