Finding .txt files that exist in one directory but not the other
That's where generators can be very helpful, for example you could use:

if args:
    folderlist = (f for f in folderlist if f.endswith('.txt') and not os.path.exists(os.path.join(folder2, f))
else:
    folderlist = (f for f in folderlist if f.endswith('.txt'))

for x in folderlist:
    full_path = os.path.join(folder, x)
    the_list.append(full_path)


The checks are now done in the "generator expression"s. 

You could simplify this some more because the if x.endswith('.txt') is done in both branches:

folderlist = (f for f in folderlist if f.endswith('.txt'))
if args:
    folderlist = (f for f in folderlist if not os.path.exists(os.path.join(folder2, f))

for x in folderlist:
    full_path = os.path.join(folder, x)
    the_list.append(full_path)