There seems to be an issue with hex S lane-switching feature, which could also be related to reports of other people having on link on SFP modules. As far as I observed, switching lane from Ethernet ports to SFP works fine, however switching from SFP to Ethernet does not - as soon as SFP module is removed and interface disabled, all Ethernet interfaces on the SFP-shared lane are dead. I’ve confirmed that by accessing device from port on dedicated lane. Disabling/Enabling ports on shared lane does not help this - they properly link up but never receive or send any traffic. Software reboots helps to clear this issue. Do note that I did not test link on SFP after hot-plug - it’s very possible that indeed same behavior is exhibited as mentioned but on SFP port.
In my opinion, this should either be addressed or reboot should be enforced when enabling or disabling SFP ports to force RouterBOOT to take care of lane switching, as obviously something inside RouterOS (most likely kernel drivers) fails when shared lane is given back to Ethernet. As a temporary measure maybe a note in Wiki article could be made to make users aware of this issue.
If this issue is not yet known to Mikrotik developers, I’m willing to share supout files from incident.
EDIT: I can now confirm that with S+DA0001 there is no connectivity after inserting module and enabling SFP port - link status shows ok and I can see packets being sent, however none are received. Such situation exists until soft reboot, after which it works fine. Once router was rebooted with module inserted, you can then hot-swap modules and keep connectivity with no issues. The lane will remain bound to SFP port until router is rebooted without module inserted. Disabling SFP port while lane is bound to SFP port causes all ports on that lane to lose connectivity - again, soft reboot solved that.