this is mostly a copy of a thread I created in a device-specific forum (original thread), but since nobody was able to answer the question there and considering it doesn't seem to be device-specific after all, I figured I'd go ahead and ask here as well. The copy & paste part begins here, with slight modifications:
A few days ago, I found that I was in dire need of some more free space on my Samsung Galaxy S4 / GT-I9505's internal storage and found that only the contents of /sdcard/DCIM/.thumbnails were taking up space. After a while of trying to get rid of those files that kept creating themselves again, I followed some advice I read on an Android forum: I deleted the contents of the .thumbnail folder, went to Settings -> Apps and cleared the data of the Gallery and Media Storage apps, respectively, before rebooting the phone.
The contents did disappear for good, but neither Total Commander nor the list of installed apps in the settings nor the Storage summary in the settings showed any different amount of free space than before. To make matters worse, the number didn't even change after I found and deleted about 1 GB of files left by an already uninstalled app, i.e. it seems to be stuck on that value. At the same time, SD Maid tells me that I should have a good 5 GB of free space more than the system is showing. Neither restarting nor wiping the cache and dalvik cache helped.
My rooted GT-I9505 is running this unofficial port of AOKP 4.3, Milestone 1, and version 6.15.6 of PhilZ/CWM Advanced. I'm not sure whether there's more information I might need to provide, other than that the size of the thumbnails files apparently exploded (about 4 GB) when I moved quite a lot of data and obb folders to my external storage using FolderMount.
I didn't find any information about this kind of problem anywhere and am afraid I messed up so badly that I might need to reflash...or worse. Do you have an idea how I can try to fix it?