Okay, You're asking a question about macOS and Microsoft Windows and SMB and AFP and icons that get displayed. You're asking specifically about why accessing files via AFP differs from using SMB. There are apparently also Windows or Windows Server systems involved here. There may be Windows clients here, and there are multiple macOS clients involved.
SMB is the default file sharing protocol on recent macOS versions, and it is supported on older versions. OS X 10.9 Mavericks and later default to SMB, and fall back to using AFP.
macOS also supports AFP, though that is no longer the default file sharing protocol on current versions.
Windows and Windows Server does not support AFP.
Windows and Windows Server support for SMB has been a moving target too, and I'd recommend running Windows 10 or Windows Server 2016 over there. They've made updates to SMB, fixed some nasty bugs, and plugged some security holes not the least of which was the entire SMB1 implementation.
Okay, now along to my confusion...
What I don't know here is what macOS and Windows and maybe Windows Server and also the software versions in use on each of these — which combinations — are in use. You've been clear that AFP works and SMB doesn't, but not if everything — on the client and on the file server — is running current versions.
I'm not sure where the testing with AFP is arising; whether there's a second file server around, or if you're using AFP on a macOS client — Mac to Mac, rather than Mac to that Windows or Windows Server system — or if the file server itself is a Mac running Server.app or running the older OS X Server software configuration and you're toggling between SMB and AFP there.
If you're on recent versions of macOS, then I'd expect that copying files around will work and that the different Mac clients will show the expected icons across all SMB and AFP servers connected. Which means this is probably worth a call to the Apple support folks. If however you're running an older versions of OS X, see if upgrading a couple of the Mac clients to current — preferably to macOS 10.12 Sierra — works as expected across the clients. Apple Support will almost certainly ask you to upgrade to current macOS software, too, so — if that upgrade doesn't work — that upgrade will still skip a step when you talk to the folks Apple Support.