In addition to what I wrote in the clonkspot forum:

> git did not exit cleanly (exit code 128)

This probably indicates a merging problem. If this is everything your client tells you, the client's not very great. However, often there's a much better log file somewhere. But my guess would be a merging problem.

New files are not endangered by pulling, fetching, rebasing, merging, etc. However edits are, there you need to commit them first or stash them before pulling. My workflow on linux (command line is):

git status (tells me I am on master and have some open edits)
git stash (stash the edits for a short time)
git pull --rebase origin master (get the newest changes and rebase my local commits on top of those, this is better than merging)
git stash pop (reapply the edits from the previous git stash command)

I found it very helpful to take two hours and read parts of the git book and note down the most useful commands for me (now I know them by heart).