I believe EncyclopeDIA accepts a .blib file. So, you could try File > Import > Assay Library to go from Spectronaut into Skyline. If you can get that to work, which it should in many cases, if you use a CSV from Spectronaut, this will cause Skyline to produce a .blib file, and you likely can use that .blib file with EncyclopeDIA. Though, EncyclopeDIA may work best with more fully expressed MS/MS spectra. e.g. Spectronaut may have reduced them to just 6 peaks.
You might want to try backing up a step to building the library inside Skyline, which you definitely can also use in Spectronaut. I have seen that Biognosys provides a Skyline report template for transferring a library from Skyline to Spectronaut.
If you use Skyline to build the library from DDA results, then you could use that .blib in EncyclopeDIA. If you have used Spectronaut to build your library directly from DIA data, however, then you are likely back to trying to get that into Skyline with File > Import > Assay Library and using the resulting .blib with EncyclopeDIA. I would just try to get as complete a set of fragment ions peaks as you can out of Spectronaut.
Hope this helps.