Well, you've made a point about 2.5 ... blah, blah, blah ... and so you must realize that most folks in these forums no longer run a 2.5 ....so ... this response from what I re-call about vr 2's of Moodle and file system repositories - which is gonna require some sluething an old version of Moodle. :|
First ... think you are going to have to query your DB mdl_files table for contenthash and filename ... file name = ReadersGuide.pptx. The content hash shows the real location of the file ... if I re-call correctly.
In the example below am using PDF's in a 3.4.x
mysql> select contenthash,filename from mdl_files where filename like '%.pdf';
renders a list ... one of which is:
| d0dea4b89feb351495f87aec30a8fa88bd1957fd | 022-201_GTE_Module_1_No_Skill_Check_NP.pdf |
Yours will have similar contenthash ...
Now find the file in the sea of files located in moodledata/filedir/
find ./ -name d0dea4b89feb351495f87aec30a8fa88bd1957fd
In my example, that shows:
That's the real file.
file -b ./d0/de/d0dea4b89feb351495f87aec30a8fa88bd1957fd
PDF document, version 1.7
shows it's a PDF.
Your file *might* be in moodledata/repository/Miscellaneous/Library Studies/Course Documents (Folder)/Files and Subfolders/MOD B
One of the options to linking to files in a file system repository was 'alias'. If, when you edit, the link to it, is alias checked?
Since your drag and drop is a filename that is the same, moodle (that old) might really ignore the new uploaded file by same name.
I don't remember where the 'alias' designator might be recroded.
So you might need to 'explain mdl_files' table from mysql client ... am looking at a 3.4 to write this so am not sure if that table structure has changed from a 2.5.x to a 3.4.
Anyhoo .... that's some old version sluething for you to try.
Also ... even back at 2.5 moodle was caching many things ... the ReadersGuide.pptx (by some obscure hashing) might be cached.
Best of luck!