Though I have never faced this, I know what is causing it, and you can ignore it. And it is probably the last time you will see it too, unless you are switching back and forth from 3.9.2 in this manner. Moreover, this is more of a bug with 3.9.2 as opposed to 3.9.5.
If you are interested, here is the rationale. Starting from 3.7.4 to 3.9.2 there was a mechanism I had to put in place due to my usage of WP's Settings API. Basically the option in which all settings go is "suffusion_options". I had a different variable that merged the contents of suffusion_options with the defaults from different theme files, which was stored in suffusion_unified_options. Now, I couldn't save both in one call, so I hooked the saving of suffusion_unified_options to the update_option hook. Now, probably due to a WP bug, there were issues in telling the update_option hook to update suffusion_unified_options only if the suffusion_options variable was being saved. However, with a clever mix of coding I got around this obstacle, with a small catch. Any time that any option was saved, the suffusion_unified_options would get regenerated.
Finally in 3.9.3/3.9.4 I figured out how to get rid of this. In this process I also streamlined some arguments of some function calls. Now, if you directly updated from 3.9.2 to 3.9.5 via the auto-update mechanism, you wouldn't see this because your template directory etc would remain unchanged. But since you are trying to switch from a theme in one folder to the same theme in another folder, that is causing an option to save (the template directory option), and that tries to execute the older update_option hook with the newer code. Hence you get the warning.
This is a bit of a maze to understand (it was definitely quirky for me to figure out), so I won't be surprised if it sounds confusing.