A file that has already been compressed by a reasonably good compression algorithm will typically not compress well if you try to compress it again with another. In fact, in the worst case, “compressing” a compressed file can sometimes even make it bigger. Many files that you use every day are already compressed. Typically audio, video, and image formats are already using compression algorithms as part of the file format. MP3, JPEG, MPG, and similar file types are all already compressed and typically do not benefit much, if at all, from attempts to compress them further.
Another less likely culprit could be
that yourcomputer could be making a system restore point after compressing / decompressing all those files check your restore points to see if they correlate to the changes
Also your drive could have become severely fragmented check your drives fragmentation.
Use caution if you are using a SSD as lots of file operations can shorten the life of the drive.