Maybe someone knows how, or for certain, but I don't think it can be done. I think it has to do with how an encrypted Save formats the space on the partition. There are a couple of workarounds. One I think will work; the other I know will work.
The easiest --that I only think will work is this:
a) Change your boot-parameter so that you can boot-up without using your SaveFile/Folder: at the end of the line beginning with kernel or linuz, change pfix=fsck to pfix=ram. Reboot. This will give you the opportunity to create a new, encrypted, SaveFile.
b) Right-Click your current SaveFile, Select Properties and note its size. You'll want the encrypted SaveFile to be reasonably larger than that; some because encryption may use some space; some giving you room for more things to store.
c) Shutdown, creating an encrypted SaveFile with a name you can distinguish from your current SaveFile. IIRC, on shut-down you'll be offered the choice of 3 levels of encryption. Only the strongest provides any real deterrent.
d) Re-boot, choosing to use the encrypted SaveFile.
e) Mount (Left-Click) you old SaveFile. Click Rox's Eye to show hidden files. Select the SaveFile's contents and copy them into corresponding folders. Such copying will only be to your 'System in RAM'. But a Save will write them to your encrypted SaveFile. You can (probably should) select one top-level folder at a time for copying/Saving.
Even if the above recipe works I would NOT use it. Creating an encrypted SaveFile formats it as Linux Ext2 which is prone to corruption. There's far more chance that it will become corrupted so that you won't be able to access its contents than that your system will fall into the wrong hands.
Encrypting an entire operating system may have some propaganda value if you are Microsoft and don't want people pirating that system. Puppy is free, and freely distributed. All its applications are free, and freely distributed. The only things worth encrypting is data you don't want others to access. Do you care if someone has access to last week's shopping list? The pdf you downloaded?
This is what I recommend:
(1) Move all data files (documents, pictures, spreadsheets, videos, etc.) out of your SaveFile. [They should not have been there].
(2) Take a look at the files-systems fossapup64 uses to boot: initrd.gz, vmlinuz, puppy_fossapup64_9.X.sfs, etc. ['X', I don't know if you have the original (9.5) or new fossapup (9.6)]. Is there an adrv_possapup64_9.X.sfs but NO ydrv_possapup64_9.X.sfs?
If so, Right-Click adrv_possapup64_9.X.sfs >select rename and rename it ydrv_possapup64_9.X.sfs. ydrvs and adrvs do the same thing, but adrvs have priority. Its content will over-ride that of a ydrv. We're going to create an adrv to hold your current settings, customizations and the applications you added. It will take the place of your SaveFile, enabling you to create a new SaveFile if you want.
[Both adrv & yrdv are READ-ONLY. A hacker can't change them].
(3) Install nicOS-Utility-Suite, https://www.forum.puppylinux.com/viewto ... 983#p12983. That post shows its GUI. Use its Save2SFS module to create an adrv, choosing to exclude your current (renamed) ydrv.
(4) Boot pfix=RAM so as not to use your SaveFile. Create a folder and move your SaveFile into it so its use won't be offered on boot-up. When you're satisfied with your system you can delete it. It's there only to enable you to revert if you find a problem.
On shut-down you'll be offered the opportunity to create a SaveFile.
Step 3a Before creating the adrv you may want to install some application to encrypt folders. Jafadmin has published a front end for LUKS, https://www.forum.puppylinux.com/viewto ... 2827#p2827. But if I read that post correctly, you'll have to use Puppy Package Manager to install LUKS, itself.
Personally, I like pzip. Easy to use and can be used other than just to create and use encrypted folders. You can obtain the Portable GTK2 from here, https://peazip.github.io/peazip-linux.html. Download it. Right-Click the tar.gz which downloaded and select UExtract. Within the extraction folder will be one with a long name. Right-Click select Rename and truncate the name down to just 'peazip'. To run it, just Left-Click the binary named 'peazip' within that folder.
You can drag/drop that folder into /opt. If you book-mark the /opt folder it will be easy to use when needed even without a menu entry. [You can, of course, create one]. When you peazip a folder you'll be asked if you want to encrypt it.