When you update from a version 2.* to a version 3.* then all elog entry files will be moved in subfolder for each year. But non of the entries are lost.

Only if you afterwards try to start an old version 2.* with the newly converted data directories, then the old version will not find any of the entries.

I've updated the ELOG version many times now. The only data I once lost was a modified CSS style file and a "hand modified" configuration of the ckeditor.