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Xcode project has lost track of file modification

I have a project which doesn't seem to be correctly recognising changes to one particular file. It is included as part of the precompiled header, but alterations in the file do not prompt the precompiled header to be rebuilt.

More worryingly, I made a whole series of modifications to the code in that header which I subsequently found had been lost. I presume that at some point and for some reason they were overwritten with an old version of the content. The only strange thing I've done with that file, a while ago, was to make a copy, trash the original, and then update the project to point to the new copy. Everything is apparently as it should be, but maybe something strange has gone wrong behind the scenes.

Does anybody recognise these symptoms? I realise the information I've given is necessarily vague, but I'd be grateful to hear from anybody who's had similar problems. The loss of data is obviously very worrying and I'd like to know for sure that that won't happen again. I'm inclined to trash the entire project and start from scratch, but that's going to be quite a task! Can anyone recommend any less drastic measures that may help?

Cheers
Jonny
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