The currently available Shine’s Savedatatool can only dump pre-2.0’s savedata. It doesn’t work on Valkyrie Profile : Lenneth’s savedata.

Thus in order to make the hard mode (which includes some interesting puzzles) easier to play, you will have to hack the iso.

Load the 677 MBs of iso into a hex editor (you’d better have loads of RAM and a fast CPU), and do the following :

Save anywhere

Find A003429401004230070040140000
Replace with A003429401004230070000100000

Find 01006330040060548000
Replace with 01006330040000508000

Freeze CP while changing Traits

Find 2328A600D00085A430
Replace with 2328A000D00085A430

Find again 2328A600D00085A430
Replace with 2328A000D00085A430

All Divine Items Available 

Find 010042305C00405001
Replace with 010042305C00E05301

Find 2A08020223002014
Replace with 2A08020201002014 

With these mods, you can get free Skill Potion or Quartz Gem to raise a character’s CP, free Lapis Lazuli to raise MP, free Material Potion to raise DME plus all sorts of goodies.

This way, you can engage those puzzles without worrying about monsters.