I have something similar happening to me.  I have been getting constant drops in external connectivity throughout the day.  I do have some pretty substantial connectivity downtime close to the same time daily, but the more annoying connectivity drops happen erratically.  If I play any MMOs or any online games, I receive frequent disconnects.  If I am testing in one of my cloud environments, the portals will hang and sometimes crash especially when working running jobs and monitoring.  Our work laptop’s VPNs disconnect randomly which can be frustrating.  I have run Wireshark pcaps, removed the VLANs, ACLs, changed out cables, rebooted all of the devices multiple times, set longer DHCP lease times, set reservations for critical devices, shutdown a couple of my hypervisors and servers, disconnected my test rack of Cisco equipment, changed my external DNS to OpenDNS, checked for loops, and upgraded the firmware on the devices. 

Omada portal is not really showing anything error-wise or anything odd.  It is definitely not showing any drops from what I could see.  I really wish that the platform had better logging.  It is very limited with the logging in the portal.  Admittedly, I am more familiar with Cisco networking/security equipment and their logging, so I may just be missing something.  Wireshark has been giving me the most information, but it is a bit difficult catching the downtime at the right time.  I would rather not run a packet capture all day, but I may end up doing that.  I am thinking that I may have narrowed it down to the ER7206 router, but I could be wrong. I am thinking about routing the traffic through a Cisco FTD for hopefully better logging.  I don't know if it will help, or if it will help me catch anything.  I am willing to try anything at this point.  I may also remove the controller from the mix and manage the switches and router separately. 

I am at a bit of a loss as well.  This only started, since I moved to using the TP-Link Omada switches, router, and controller especially the router.  Inter-subnet traffic seems fine.  It mostly appears to be external but some issues with traffic crossing VLANs. I am noticing the issues mostly with http/https traffic, since it is more frequent.  I do notice issues with email clients disconnecting or application hangs during connection.  I have a server which replicates folder changes up to the cloud, and it also has intermittent issues but that is all http/https. My significant other and I work primarily from home, so it is critical to have consistent connectivity.  If I don't have it resolved soon, I may have to call this purchase a wash and roll back to another solution. 

Has your issue resolved at all?