The following error messages may be sporadically generated when clicking Merge and Box in Conga Composer:
There was an issue processing the Composer request.
The remote server returned an error: (409) Conflict.
A common reason for these errors is having more than 1,000 folders included at any given level of the Composer document's output file path (see OFP for more information). This is because the API call Box makes has a limit of 1,000 folders, so Composer is unable to query for folders beyond the 1,000th folder.
What to Do
The solution is to ensure there will never be over 1,000 folders at any given level in your Box account.