when you initiate a download configuration on the lmce side, it will replicate the network information from a controller. LMCE sets the SIS (static update controller with node id server) flags. When you have a recent portable controller, and do the download config step, it will enable the sis. **But it will also remove any stored network information from the dongle on the lmce side**. It will also use the network id of the portable controller. When all your controllers were reset, the portable controller will have node id 1, the static controller (dongle) on the lmce side will have id 2. You then usually start to add other devices.
When the static controller on the lmce side shall be the primary controller, you just send the "reset" command to it with the web admin. It is then the primary static (update) controller (with node id server). You can then use the "add node" command from 0810 to add any inclusion controllers. The static controller will then have node id 1 and use its own factory programmed network id. After that start to add your other z-wave devices. I prefer this approach but it needs 0810 as the add/remove node commands needed for primary operation were not present in 0710.
As you've "lost" your old remote, and you got a new one without any network configuration, you've replicated the "empty" network to the dongle. That is why you've "lost" all devices. Reset all your z-wave nodes and re-add them after doing one of the above initialization methods.