There's not sufficient information here to diagnose the problem, but if you're uploading a 2.9GB file to a memory store, and the size of the memory store's storage dir is only 125M, that probably means that your data has not been persisted to disk. You likely have not configured your in-memory repository to sync to disk, or something has gone wrong during upload.
And no, the in-memory store does not use the native store's persistence mechanism, it has its own (far less sophisticated) persistence mechanism.