3 days is enough. The gentle air exchange will have begun to aclimate the foliage to the outside air. I'd deflask tomorrow.
Here's how I do it. The following are photos of the seedlings from two Cattleya flasks and one Phrag flask. They have been removed from their flask with the agar intact and roots undisturbed. They were potted like this. I did not remove any agar. In fact, one of the clumps lost a large lump of agar, which I put back before I com-potted the whole lump of seedlings together.
Photo #1
Three bunches of seedlings immediately after removing them from their glass flask. The agar "puck" is left intact.
Photo #2
All potted up. Those are 6" clear plastic pots. Notice the ample amount of styrofoam peanuts in the bottom for drainage. The mix is 1/2 filtered perlite and 1/2 small size CHC.
Photo #3 and #4
If you leave the seedlings fully exposed to the air and the air movement, they will likely go soft and wilt and suffer great stress. The pot on the right would suffer greatly. However, I have cut the bottom out of a Margarine tub and taped it over the pot to create a "cone" that will contain a microclimate of less air movement and much slower air exchange. It also reduces and filters/softens the light. Unless the sun is directly overhead, which it is not, the light reaching way down inside to the seedlings is reflected in through the top and filtered as it passes in through the white, plastic sides. However, the open top still allows for heat to escape and excess humidity to escape. It also allows for easy inspection and proper watering. This more gentle, less extreme microclimate is a very good "nursery" which allows seedlings to aclimate at their own pace without losing ground and being stressed. The seedlings in the photo were planted out on April 13. Now, it's May 20th and they have never shown any signs of stress, they've never gone soft, never wilted, never lost a single leaf, never developed brown edges and not even one seedling has been lost. After 5 weeks post deflasking, they're all strong, turgin, healthy and thriving seedlings. In another month, I'll remove the "cone" tops and they'll begin to take off with new growth.
As I said, the cones will be removed after a couple months. However, the seedlings will be left to grow and put on some size, for about 8 or 12 months. By the time the compots are unpotted and the seedlings given their own, individual pots, the agar will have long since disolved away and disappeared.
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