The context menu (rght-click) in the Project Explorer has a ‘Rename’ option. If this is used to rename a file, the Project Explorer display doesn’t update - you have to manually refresh it.
Edit:
Actually, if you’re renaming a number of files, it does update at some point - which gets rather confusing, as you never know quite where you are…
Eclipse’s stuff…
Seems to be random, since it is usually refreshed correctly (but it’s true that sometimes not…)
I’m getting a bit sick of this excuse. If I buy a car from Ford, and the tyres keep failing, I don’t expect them to say to me “that’s a known problem with Michelin tyres”, I expect them to fix it. I don’t care if they make Michelin fix the problem, or they start buying tyres from Dunlop, I just want the problem solved.
Additionally, Sierra Wireless has a 3rd option, which Ford does not. Eclipse is open source, so the M2M studio developers are free to fix things themselves.
One point for you 
I didn’t want to discard the issue: generally speaking we’re doing our best to resolve such cases by implementing a workaround, or pushing hard on Eclipse side to get a fix if it’s not possible.
In this particular case, the behavior is so random that even on our side it will be hard to reproduce (and then to find a fix, or a workaround, or to explain to Eclipse guys also how to reproduce it)