I often get an issue when shooting events where the file names roll over from 9999 to 0001. You might get this on holiday or during a long shoot.
All the files are unique, but they get out of sequential order.
Here's a little bit of software that can solve this issue that Phil Wilding brought to my attention.
Bulk Rename Utility
It's free to download here and use and has lots of uses based around mass renaming of files.
So say you have _319999.CR2 and _310001.CR2 for instance. The latter was taken after, but will come before the former in any file listing or Bridge. (Canon RAW file names used, but the principle is the same for all manufacturers)
Using BRU there's a replace option. So highlight/select the files _310001 through to your last shot, say _310350 and replace the _31 to _32.
(_310001 becomes _320001 etc.)
Then the images shot later will come in the correct chronological sequence in your file structure or Bridge and things are a lot easier to understand.