To spell it out, JCS didn't overwrite this data. As it does not contain recognizable patterns, we do not know what the corrupted data represents. However, as far as we call tell, half of the file has been completely wiped out and replaced with data that is unrelated and not part of your JJ2 level. The original data is not in this file. The corrupted data is highly unlikely to have been caused by JCS. It's hard to tell for sure, because we do not have the source code of JCS, but the fact that the data goes incorrect in the middle of a compressed stream rather than for the entirety of it suggests this.

If not by JCS, it must have almost certainly been done by something that's part of your operating system. Files having part of their content overwritten is never normal behavior. Files are stored in data clusters, essentially small pieces of your hard drive, which nowadays are usually 4 KiB in size. Files bigger than 4 KiB must be stored in several clusters. Your file becomes corrupted after around 4 KiB, which may be a coincidence, but may also mean it's attempting to read a cluster that doesn't belong to it, or something happened to the cluster that was supposed to contain it. If this is really the case, there may be a bigger problem with your file system. Such problems may be caused by many factors, from unsafely removing USB storage to power cuts.

CHKDSK is a Microsoft utility that's available on every Windows operating system. It tests integrity of the file system, for example by checking if what the file system thinks about where files are located on the hard drive makes any sense. It's also capable of fixing some of the problems it encounters. I'm not saying it will fix your file, but I am saying nothing else will, so might as well run it. More importantly, it may detect problems with the file system that you didn't run into yet. The Internet will offer you instructions how to use it. If you use several drives, physical or virtual, remember to choose the one containing the file.