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It sounds like the seeds are sensitive to the light. You don't need to cover the seeds and seedlings; in fact they need light to germinate.

You will need to slowly harden off the seedling. Slowly add light until you can keep the seedlings in bright sunlight as they develop. Repot them into individual pots as soon as they are large enough to handle. Fertilize repotted seedlings with liquid fertilizer diluted to half the recommended strength.

These articles will help you.

https://www.gardeningknowhow.com/ornamental/trees/royal-empress/pruning-empress-trees.htm

This can be common in areas that are at the edge of its native climate. This is no worry, and is the natural cycle in your area.

This article will give you more information: https://www.gardeningknowhow.com/ornamental/trees/royal-empress/worlds-fastest-growing-shade-tree.htm

Can you include photos? This could be an insect, but depending on how the damage appears it can also be a shothole fungus.

In the meantime, this collection of articles will give you ways of controlling fungus and insects with ingredients that you likely already have around: https://www.gardeningknowhow.com/special/organic

Royal Empress Trees have some wonderful qualities, though this tree may not be for everyone.
We are an information site and provide detailed growing information.
We suggest talking with your local garden centers or even your County Extension Office for the most suitable trees for your area.

Check watering and make sure the soil is well draining.

There may have been some root death and part of the tree is not receiving water.