I can verify their existence, but you don't need to take my word for it - much of the research on fully homomorphic encryption is publicly available through the IACR's online preprint database,
http://eprint.iacr.org . I doubt FHE is a good solution for your project, though. The technique is not quite ready for primetime due to seriously slow performance. It gets better every year but it will be a while yet before you'll be able to diff an encrypted file using FHE.
EDIT: Though now that I think about it you might be able to code a custom diff circuit for FHE that borders on feasibility. It depends on the algorithm used, really. File diff seems spiritually similar to some of the bioinformatics work being done with privacy-preserving edit distance computation on encrypted DNA sequences.
EDIT2: Here's a paper that discusses an FHE 'hardware platform': http://eprint.iacr.org/2014/106.pdf