>It is strange to me, how could git folder just lose.
>For tde-i18n would "lost" had to take some time.

Strange to me too and I've had all day to think about a root cause. 
I know of only one thing I might have done to inadvertently delete 
the folders. Yet the conundrum of even that possibility is every 
single .git folder should have been deleted throughout the entire 
tree. That is not the case. Further, stand-alone files such as 
.gitmodules would have been deleted too, but those files are intact.

Other than the .git folder the remainder of the tde-i18n module 
tree is intact.

>Have you tried git fsck on the modules that are okay for now?
Yes. I also tried git clean -f.

Running 'git pull' results in an 'Already up to date' message and 
no errors. When I run the switch_all_submodules_to_head_and_clean 
script then the proverbial hell breaks loose because some of the 
modules are missing the respective .git folders.

At this point I just want my local tree updated far more than 
solving the mystery of what happened.

Further frustrating is the Trinity git server is really slow with 
respect to cloning. According to the progress bar, I'm downloading 
at about 80-90 KiB/s. At 1.1 GB and a 3 Mbps connection, the tde-
i18n module should finish loading in about 50 minutes. I'm still 
waiting 90 minutes later and the tde-i18n clone is only 64% 
complete. At this rate, cloning the entire tree might take days. :-(

Darrell