When a symlinked file is opened from the linked location Geany 0.2 deletes the symlink and saves the file in the directory. Geany 0.18 didn't have that problem.
Can not reproduce the issue here, unfortunately. Created a file test and a link test2 pointing to test. Opened test2 with Geany, edited and saved, test2 is still there as link and test contains the content I entered. Running Geany from SVN revision 5530.
The reason you couldn't repro is (I think) that it isn't a symlink that's the problem, it's a hard link (made with mklink). If Geany deletes the original file and renames a temp file to the original name, that would probably cause the problem. This is my problem with Geany 0.20.
Do you have the use_safe_file_saving hidden pref enabled?
Geany file saving default changed (for safety) produces the behavior described but with hardlinks not symlinks, described problem could not be reproduced.