As other answers say, most of the time your best bet is to work with Perforce's workflow and check out the workspace in advance and make your changes there, rather than make changes first and create the workspace later. Sometimes, though, you really do need to break Perforce's workflow and override the changes in the depot. If you're going to do that, you need to be extra careful that you're not reverting something important. (Even on a one-person project you might have forgotten you checked something in, so look carefully at the diffs before submitting.)
The easiest thing to do is, when Perforce tells you that you have a conflict, resolve but keep your changes. In the Perforce documentation link, that's 'resolve, accept yours' rather than accepting what Perforce thinks is the sensible merge. From the command line, that's p4 resolve -ay. It's worded a little differently in the p4v GUI, and may be worded differently still in the Eclipse plugin (which I haven't actually worked with).
The other option, which you might use if you have files checked out from an earlier revision, and you want to update to the tip revision without making any changes, is to tell Perforce to update the metadata, so that it thinks you have a newer version of the file, without actually altering any of your files. From the command line, that's p4 sync -k (whatever you want to sync). This, too, can be dangerous if used inappropriately.