So Special:SMWAdmin > "Data repair and upgrade" "offers a feature to restore all Semantic MediaWiki data based on the current contents of the wiki". Where rebuildData.php "recreates all the semantic data in the database".
What exactly is the difference (besides working command line or not)? Is there any difference? Or just calls Special:SMWAdmin the rebuildData.php script?
We're using SMW 2.2.
The essential difference is that Special:SMWAdmin only ''queues'' the updates in the job queue, while rebuildData.php actually performs the updates.
If your job queue is correctly configured, the difference may be trivial; otherwise you'll run into performance issues. A common error is to have insufficient memory for the job runner. If all else fails, the last resort is null-editing all the pages.
The difference was actually written in the help page, but in a weird English; fixed that too.