Yes (assuming your .subs are text-based subs) you can merge, making use of one of the subtitle utitlities mentioned in item 9 of my Help2Help-post.
E.g. with SubSync (if necessary) make sure subtitles of 1st sub-file "sync" with 1st part of the movie; then "sync" 2nd subs with second part of the movie. (Both parts to be saved after "sync"-ing them of course.)
Then open 2nd subs (as saved) in e.g. Wordpad, select whole text and "copy". Then open 1st sub in Wordpad, scroll to the end of it and now "paste" (making sure there is one empty line between the last subtitle of the 1st part and the first subtitle of the 2nd part, just like between all other sub-lines) and save the file. Load the new (total) file in subsync and save it (you have to do this, simply in order to renumber the subtitles in the file). That's it.
The two other subtitle utilities I mention in my post also can merge subs. However, you will have to find out the procedure to follow with these utilities yourselves, as I don't use them myself.
Perhaps it might be easier for you to find 1-CD-version subtitles for your movie. What movie is it?
