Personally I feel it's absolutely fine if they are not as risk of getting damaged. I keep mine it plastic boxes with lots of compartments, ill think about how I'm matching them purely based on if they could get damaged. The mixing of energies would only really be an issue when you was using them, if you have one that is giving you a boost of physical energy and another is relaxing you... it's natural you can't possibly feel the full effect of either.
You can't ruin healing energies in my opinion either. If they start feeling a little flat when your using them cleanse and charge them.
Just be careful putting them in the jar and getting them out if there are many in there. Maybe you could put something like cotton wool as a bed... or even some lavender or something. Something like lavender would be good for crystals too
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