We are using Lyra as a test bench for some stuff and I have had problems every time I need to update to a new engine version.
The root issue seems to be that at boot time, when FModuleManager is resolving where each piece is, it gets confused by having both my outside Lyra copy and the engine’s own Samples/Games/Lyra directories. The end result is that it looks for the editor modules in the (wrong) engine workspace rather than my external copy.
I have since “fixed” this by just moving the original Lyra somewhere else but I wish it had been easier to find out what was going on there.
You should be able to have multiple copies of Lyra around. I was able to reproduce the problem and track it to a change that was added in version 5.3. I logged it as a bug so it can be addressed in a future release.