Metal drainage grate, available off the shelf, or will need to have it custom made

My initial reaction is that it is still moisture from the January incident.

Concrete can be water-tight but most poured slabs are still very porous and water will seep into many of tiny bubbles of the concrete and persist for a very long time. Though the remediation company may have come and dried the floor, the slab may still have water and it is evaporating. Replacing the floor too soon may have just trapped the moisture, slowing its drying and placing your flooring into nearly direct contact with the moisture, barrier or not. Your climate could affect this too, live in the southern US for example it is going to take a lot longer to evaporate than in Colorado.

I personally would rip up the flooring, buy just a consumer grade dehumidifier and run it for a few months; wait a month without it running and then test for moisture again. Testing the sheetrock near the floor with a hydrometer will also help determine if there is a moisture problem too.

It is a pain, but the pain and patience will protect your investment. Selling a house with suspected mold is not always easy, but not disclosing the damage is also risky.

By drainage problem you are a bit vague... or they were. If it is a problem with the sanitary line, it might require a plumber to determine that and at worst, digging up the slab! Drainage problem could be also that your landscaping is holding water up against the house which eventually could make its way into your living spaces as moisture.

One other thought.

If the flooring had been reinstalled in the winter, it could be the changes in humidity that could be stressing your flooring. But given your situation and what some professionals have told you, I would find it unlikely.

Those typically act as temporary rain water water storage tanks. The idea being to limit the demand on the sewer system during storms. The water is allowed to back-up in those pits and drain more slowly to the sewer system. They may also be used in high water table areas to collect and drain the water table before the water enters your house during the rainy or snow melt season.

You have a few choices.

You could fill it with rocks, but that would take away a lot of volume and defeat the purpose of the pit so I do not recommend it. That may also be against code in your area.

You could cover it with a grating, perhaps made from metal fencing materials or a custom grating, but that wont look that wonderful and is a pain to clean out leaves, blown in trash, or someone's cigarette butts...grrr.

You could, put a fence around it to stop folks from falling in, but again, that's a bit of an eyesore and the cleaning issue.

Personally I'd cover it entirely, leaving an air hole in the side and access to the maintenance pipe cap shown in the image. Perhaps composite decking or some other material, then make a feature out of it with planters.

My personal, preferred solution would be to turn the "decking' into a box, that is make the entire decking one big attractive planter over the open box. Would be a fun project too :) I'd make the sides of the box match the cladding I see on the wall behind. I'd also extend the maintenance pipe up through the box so you can get at it without having to remove the planter. Maybe have it end just under planter soil level.