Unity messes up the fileIDs

I’m working in a team of three people on a 2D game, and Unity recently has been messing up the fileID on many sprites:

-  m_Sprite: {fileID: 21300000, guid: 6186fa4d068aae8418d9520f658d1ee6, type: 3}
+  m_Sprite: {fileID: 21300002, guid: 6186fa4d068aae8418d9520f658d1ee6, type: 3}

The guid stays the same, but the fileID changes, and the sprite goes missing. If one member fixes it, it becomes broken for one or both the others.

What can we do to fix that?

“reimport” didn’t work. Prefabbing them didn’t work either.

We are using 4.6.0f3, and before that we were using 4.6.0b17 IIRC.

Please submit a bug report following these guidelines:

If possible attach a sample project that reproduces the issue, that would be very helpful.