For the matter of PKG signatures there is no step back, the original signature of the PKG is special and only sony can do it
If your goal is preservation of original files you need to keep a copy of the original PKG
Also, think of the PKGs as software installers. It will copy its inner contents into the console to different paths, and execute actions to register the changes made.
So, plus what @sandungas said before, it's impossible to remake the PKG from files already installed in your console. Better have copies of your PKGs.
If you do not want to restore the original sony signing of the pkg that would allow it to install on OFW, and just only to backup the data for installing again later..
Then simply dump the dev_hdd0/game/XXXXXXXXX/ folder.
Where XXXXXXXXX = the content ID of the app.
Then make a PKG file out of the folder if you want, or just keep it like that. it will be 99.999% the same as the original pkg apart from the pkg signing which does not matter most of the time.
If that folder is copied to /dev_usb000/GAMEI/XXXXXXXXX, the game can be launched directly from the USB (with a few exceptions) using webMAN MOD.
A limitation is that the folder should not contain files larger than 4GB and the USB device must be formatted in FAT32 MBR.
If the game has NPDRM, you will need to backup the .rif files in /dev_hdd0/home/00000xxx/exdata or copy the corresponding .rap file in /dev_hdd0/exdata or /dev_usb000/exdata