Erm... I've to reopen this thread, because generating code on top of old generated code should work, it should pick up the user code generations and migrate them.
If you make a copy of the v2.6 code, generate with 3.5 on top of that, it should work and generate v3.5 code and migrate the user code regions.
What it doesn't do, is convert your own code to use interfaces which changed. Most methods are still there though, they're just implemented explicitly, e.g. you have to cast to IEntityCore or IEntity/IEntity2.
As long as the code is in user code regions, that code should be migrated to the v3.5 generated code, as long as you generate that code on top of the 2.6 code.
be aware that some classes have been removed in v3.5