The question here would be whether you want to preserve history. If you do and if the file names do not conflict, then probably you can copy your metadata over into the new wiki. Then you should get the searchindex plugin and recreate your index:
If you put your files into a new namespace, then you won't be able to reclaim the history for those files. You can copy the metadata into the new namespace but any backlink information and anything else that uses path information wiil be incorrect.
If you don't care about these things, then you can simply merge the two data/pages directories, as long as (as Ashtagon has said) there are no overlapping file names. The you can run the searchindex plugin.