If I understand your problem you have upgraded to the version 1.3.1 but may not have copied your modified theme over to the newly upgraded themes directory. In other words, if you had adapted the 'standard logo' theme and replaced the logo.jpg file with your own logo, when you upgraded a new version of the 'standard logo' theme was installed.
If this were the case you would need to send copies of your modified logos into the 'standard logo' folder inside of your themes folder. This is assuming that you made modifications to an existing theme without giving it a new name. If you created a completely new folder based on an existing theme then you will need to place your modified theme folder into the themes folder so that you can use it.
In my installation of moodle I made a copy of the 'stardard logo' folder and renamed it 'MyTheme'. I replaced the default logo with a new logo that I created. Now whenever I upgrade my moodle I need to copy my modified them 'MyTheme' into the themes folder in the new moodle installation.
I am at risk of writing a whole dissertation here so I'll stop. I hope that this helps.