Interesting that several times when I had the problem with Eclipse to load elf, i opened command shell and was able to load elf into my fpga. That is to say the problem related with the IDE (Altera SW SBT). I recall that in the past i experimented with opening another project when i had problems to load elf with a current one and it also worked for me. I use version 18.1, i would consider upgrading the Altera SW SBT if i knew the issue was addressed and resolved , but i failed to find this issue in the release notes , therefore i don't want to waste time on moving to a new version that won't release my problem.
Thanks