Warcraft III Replays contain two values which give a hint on the patch version the recorded game was played on. One value corresponds to the minor patch number (i.e. 26 for the current patch) and the other one to the replay build number (i.e. 52240 for the current patch). With those two values we can determine exactly which game version is needed. But there is of course an exception: Patch 1.24! In thise case both numbers are equal for all sub patches, even Warcraft III itself can not distinguish between those.
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If the required patch version and the currently installed Warcraft 3 Patch version do not fit, RK starts patching. Therefore, it searches for an appropriate patch in the ReplayKitPatch.mpq. When this search succeeds, the patch is applied.
In this mpq are several patches stored.
Most likely only war3.exe, game.dll, storm.dll, war3patch.mpq and all the maps differ between two versions, plus some irrelevant files, which do not effect viewing replays. All of these files are stored in the MPQ together with a recipe for every patch. The recipe is needed to recook the patches later on.
In order to reduce the data set a sophisticated way of compression is used which decreases the size of the archive significantly! All files are put together in a large pool. This way, duplicates can be omitted efficiently.
The Backup MPQ contains all files which could get destroyed by RK. With these files and a recovery recipe it is always possible to recover your original game files at any time. This backup is created automatically.