[Owncloud] Total Failure update 5.0 --> 5.0.3

[kadafax at gmail.com]

Hello list,

I am in big trouble. The spec:
- Centos 6.3 fully updated on 6 core CPU (X5675  @ 3.07GHz) and 12GB RAM 
(xen vm)
- Owncloud 5.0 with mysql backend
- 250k files (40 users)
- 1 user has 113350 files

I'm updating directly from the tar.bz2 file on the server with rsync.

All my update experiences have been problematic since 4.5 (like always 
forced to put maintenance mode to false manually), but at the end of the 
day it was working. But this time it's a complete failure.
First I tried to go from 5.0.0 straight to 5.0.3. My mysqld process went 
on 100% on a CPU for 24 hours. While "stracing" the pid I can see a lot 
of this:
read(99, "\3\0\236\2\fLotsOfFilesUserh/c", 20) = 20
pread(99, "lientsync/Folder/DocumentC"..., 142, 11140924) = 142
lseek(99, 11141068, SEEK_SET)           = 11141068

LotsOfFilesUser is the user with 113350 files.

Nothing in owncloud.log, neither in apache's logs :(

So I have killed the process this morning, went back to a working state 
with backup from 5.0 and tried to upgrade to 5.0.1 then 5.0.2 and *bam* 
same problem with 5.0.2 :(

What should I do ? Thanks for any pointer as I dont know if letting this 
process running for the whole weekend will do anything good or if it is 
normal that updating owncloud can take several days :(
Should I remove the user with 113k files ? If yes how (without 
interfering with others users) ?

Thanks,
kfx