Not that you need any more advice, but maybe a brief explanation is in order ...
In 1.9.x data folder there were course ID folders and all files related to a course could be found in there. That is no longer the case in version 2 of Moodle. Now, all files are hashed named and placed in 'filedir' of the data folder. The migration doesn't handle metadata folders in the course ID folders - user icons - and may as well clean up files in backupdata - those are 1.9 backups and won't serve any purpose in mirgration. Might also reset ALL courses ... users won't migrate anyway and resetting courses also removes assignments which might be files uploaded by users.
Here's kinda what filedir looks like now (no course ID folders):
[root@sos filedir]# ls
01 0b 1a 2a 38 46 55 71 7c 98 ab b4 ce e2 warning.txt
02 0e 1d 30 3a 4e 5d 72 7d a1 ad b6 d1 e5
09 0f 1e 32 40 4f 63 78 7f a3 b1 c6 d5 ed
0a 10 23 37 42 54 67 7b 89 a9 b2 c9 da fb
Files uploaded (or migrated in your case) are recorded in the DB with a contenthash and pathnamehash in the mdl_files table and the 'physical filename' is changed to a hash named file with no extension.
Example of '01' directory above:
[root@sos filedir]# ls -lR 01
01:
total 4
drwxrwxrwx 2 apache apache 4096 Jul 24 21:39 3e
01/3e:
total 4
-rw-rw-rw- 1 apache apache 2119 Jul 24 21:39 013ee7039a7ec06834ecd2798d99cb210aeaa5ab
This:
013ee7039a7ec06834ecd2798d99cb210aeaa5ab
is actually a file by hashname and it is a PNG graphic.
head -n 1 013ee7039a7ec06834ecd2798d99cb210aeaa5ab
will show: ?PNG
So files are physically there, but not by any re-cognizable name (ie, as they were uploaded).
There could be remaining some course ID folders in moodledata ... those will probably contain a metadata folder and one might find an assignments folder also there ... with numbered folders which were assignment ID numbers and numbered folders contained therein - which were the folders for the student by id number. This from memory and 2.3 might have gotten better about cleaning up junk it can't use.
Just one piece of advice on your next attempt at migrating ... clean up a copy of the 1.9 ... *throughly* - not only DB but any add-on, all course backups in backupdata, any 3rd party add-on mod or block. Make it as bare bones as you can with 'stock' or 'core' Moodle.
In your second post one can see a warning that certain blocks IF they had changed permissions might cause issues.
From personal experience at a migration, I eventually removed many visiable blocks from front page, from courses, and removed any add-on known NOT to have made the 'trip to 2', etc. before attempting migration. Increase variables for php and even for MySQL.
Eventually, was successful ... although still ended up with the dreaded 'Legacy file system' active not only on the front page but in every course as well.
It's a challenge ... but along the journey one will learn a little more about what makes version 2 tick (something we unfortunately/fortunately) did not have to learn with previous versions of Moodle (until forced to).
'spirit of sharing', Ken
