Why does opening a file and saving it fix a 404?

I've been unable to phrase this question in a manner that google will give me an answer. So here i am...

Randomly i get a 404 error in my website. Usually related to some changes I've been making.

Now I've done an SVN update, and suddenly I'm riddled with 404's on random pages. So i start to do the routine and first check if the guilty .jsp is missing. It's present. I check the guilty controller. It's present.

The solution is opening the controller. Adding a space anywhere. Delete that same space. Save the file. Finally restart the server. Which changes absolutely nothing in the file. Yet it makes the 404 disappear and the page opens as intended.

I have also had problems with images suddenly not being recognized. The solution is removing them from the project. Re-import the images. Restart the server.

This is something that has been bugging me for a long time now. I asked my colleage as to what is happening and he is very familiar with the problem and states "Java is just fucked that way". I really want a solution or at least a reason as to why this is happening.