Luca,
Sorry,I was looking at the Source Code-sqlite-amalgamation-3.6.11.tar.gz.
Looking at the version histories
http://www.sqlite.org/cvstrac/rlog?f=sqlite/VERSION
there looks to be two major updates 3.4.2 to 3.5.0 and 3.5.0 to 3.6.0, all the rest seem to be mostly bug fixes,
If you are concerned that installing these upgrades will install completely new data bases next to the older ones, maybe try setting up another volume to observe and test the new upgraded versions out before running them on your main volume.