If you merge records that have attachments, the documents remain attached to the new, combined record.
For example, let's say you have two customer records: Sunny Diner and Sunshine Diner. You have an estimate attached to Sunny Diner, and a receipt attached to Sunshine Diner. When you realize that these are the same customer, you decide to merge the two records into Sunshine Diner.
Both attachments—the estimate and the receipt—are now attached to Sunshine Diner.
If you don't want any of the attachments, you can detach them from the record, or remove them from the Doc Center.