Hm, are there no savegame files, or does the PC version just not recognize them?
From what I could gather, Joiplay places savegames in
> SD card>Android>data>cyou.joiplay.renpy>files>(game name)
From what I've read, Joiplay might also place or name the saves folder differently than the PC version.
If a folder with .save files exists, make sure that on PC the subfolder with them is called 'saves' and placed inside the 'game' folder of TM.
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That's strange indeed.
Is it possible to see and copy individual files from the joiplay save folder?
If you managed to copy your latest .save file and the persistent save file to your PC, you could just copy those into the saves folder of your PC version.
Also, make sure that the save folder isn't just in a different subfolder or named anything different than 'saves'.
If a folder with savegames is there, but not exactly in the right place and with the right folder name, the game may not recognize it.