If you don't mind that secure_store.dat will be a zipped file then you can use standard Java handling for zipped files...
Edit:
When you add multiple files together into one single file you must store them in such a way to preserve their boundaries, if you fail to do that the two or more files will become garbled mess.
java.util.zip functionality provides all features that you seem to need, it will create a zipped archive file with separate entries for each file that you add. It provides functionality to add/extract/remove files from the archive too.