Well...I had similar problem when I came in Doha couple of years ago. Due to perspiration my finger prints were not coming on scanner and then they did it manually with ink. Yes, indeed it is possible to get fingerprints using ink (however, I am not sure what is their current practice, but I am sure that they must have come across similar cases and would definitely have alternate plans in place).

Why dont you take this with your sponsor/employer?

Hope this helps.