I was using yesterday filebox and suddenly my n900 turned off. When I have powered it on again, I noticed many unneeded changes:

1. Additional icons on my screens - I have remove them.
2. I lost all my bookmarks in internet - I have tried to restore it from my back-up (created not so long ago) but with no result - error occured.
3. All my past phone connections was deleted - it doesn't matter to me.
4. Filebox lost icons - button are functional, but with no graphics on. I have tried to reinstall filebox - nothing has changed.
5. In my status bar still flashes icon reminding me of some application updates. I used gconf do extend period of checking time to 1 year (as I have done before using some advice from this forum). But it didn't help at all. Even when I click "Ignore" this icon still flashes.
6. My HAM lost functionality (no applications seen)
7. And many others things probably happend - I had no time to inspect it.

Does anybody know how to restore my previous functionality without flashing device?

Were you using backupmanager? I hope so as you can just use a recent backup image you saved onto SD or another machine.
I suspect you were doing some intensive writing to your MyDocs and pretty much killed the usability of your swap which is on the same chip and i/o. There are swappolube hacks to work around the i/o issues writing to internal memory.

I suggest mounting your drives to another computer and cleaning out the file systems as you seem to have had much kludging of your file system. Recover what you can and then reflash to get a stable system. Don't forget backupmanager then make and save backups off of your N900.

In addition to what biketool said, I can attest that I had numerous reboots caused by one file manager or another. Copying a large file is almost a certain killer. It does not matter where you copy it, SD or internal storage. The reason is that the OS does not go idle often enough during a long file operation and the watchdog kicks in and reboots the phone. It is definitely the application's fault: I reproduced it myself in my own application that I was developing. The stock File Manager does not suffer that problem.

An unexpected reboot can cause a serious havoc with the file system. Especially if the reboot took place during a file system operation. A corrupt file system can cause exactly the sort of symptoms you describe.

If you use BackupMenu, I recommend using it ASAP to export all your partitions and check them all on a big PC. Even better, if you have a recent backup, just save yourself a lot of trouble and reflash the system, then restore from the backup.

A backup would be the only true way to recover from this type of thing.
The default backup tool would recover most of this stuff if you had a backup. Backupmenu is also another option again this is little help if you have no backups.

You may be able to recover old backup files hidden in your device manually. rtcom-eventlogger would have an old db for example.
HAM and your notification of updates will hopefully fix itself if you run the updates with the standard repos enabled.

I would recommend using hamsterfiler over filebox. But you may recover filebox by removing all it's files manually then reinstalling.

Because the corruption is unknown normal recommendation is to flash to have a clean system going forward. It may cause all sorts of fun in the future.