Overwrite .user,ini deletes custum settings, also when updating

To avoid the message that there is not enough PHP memory available, i’ve added this line to .user.ini

memory_limit = 512M

I do not want this setting to all users and sites on our VPS, so that should be done per user.
But after updating this setting is deleted.

This is a bug, or give an instruction to avoid this unwanted behavior plaese… I could not find it in the documentation.