Hugh Vincent's file with some of his invoices cane be found on microfilm in the Confederate Papers Relating to Citizen's and Business, National Archives Microcopy M346.
There are 1158 rolls of film in this grouping and they are broken down by alphabetical listing.
The bad news is that there's only a very few places that have this film: National Archives in DC, Wallace State College in Hanceville, AL and I think one university out west - there maybe be a couple more.
There is no such thing as a complete list of flags that Vincent made, which tended to be for forts, etc, since he was a ship's chandler/sail maker before the war and thus used to working with large scale pieces of cloth. A perusal of wartime Charleston newspaper will also yield some flags that he made.
Hope this helps.