Delete or ignore I/O from a schematic block in Lattice?
You cannot delete IO from a block, but ignore them. Some warnings may appear, but sometimes they are not important (always check!). The best solution is to program your own block and select the signals you want to use. 

The error with my clock was, that I did not placed it in the main schematic. So everything was fine until I tried to download it to my target system. Always put the clock in your main schematic part. Check the hierarchy diagram so you know what is the main part.