EF core Dynamic Linq comparing Lists in a where clause
Assuming that Ids in your filterSecondaryConditions has unique values, you can use the following:
if (filterSecondaryConditions != null && filterSecondaryConditions.Count() > 0)
{
query = query.Where(w => w.SecondaryConditions.Count(s => filterSecondaryConditions.Contains(s.Id))
== filterSecondaryConditions.Count());
}