I didn’t put the lid on the slow cooker(crockpot) for first hour of beef stew. Will it still be safe to eat

I assume that the section of the USDA article you're referring to is this:

Partial Cooking
Never brown or partially cook beef to refrigerate and finish cooking later because any bacteria present wouldn't have been destroyed. It is safe to partially pre-cook or microwave beef immediately before transferring it to the hot grill to finish cooking.

Before I go on, I should point out that the USDA obviously has much greater expertise than I do when it comes to food safety. Nevertheless, I find this recommendation to be extremely bizarre bordering on silly.

For full cuts of beef (not ground beef), bacteria should only be present on the surface. That is why most people - or at least most people I know - choose to eat their steaks rare, or at most medium rare. The "interior" is not fully cooked, nor is it supposed to be.

Searing the beef will kill any surface bacteria almost immediately. That is why rare steak is (relatively) safe to eat. As far as I am concerned, once the beef has been browned, it is already cooked sufficiently. The only reason to add it to a slow cooker later would be to tenderize it or even out the cooking.

If the USDA expresses concern over refrigerating beef that has basically been cooked sufficiently, it must be because they believe that browning/searing kills enough of the bacteria to make it safe for direct consumption, but not all of the bacteria - such that they could multiply again and contaminate the food over a long period of time.

But refrigerating immediately after browning should prevent that. No part of the beef will be in the "danger zone" for longer than 45 minutes or so, and even if you did miss some of the bacteria during the browning and they manage to multiply overnight, you're still tossing them into a slow cooker and that's going to kill any remaining bacteria.

Perhaps I'm missing something obvious, but from what I can tell, any health risks associated with browning a large cut of beef and subsequently refrigerating it for a relatively small period of time would have to be infinitesimally small. It's not something that I would concern myself with.

Edit:

I did just think of one other possible reason for the USDA warning. The key phrase is "partially cook." If the browning is being done as a means for shortening the subsequent cooking time (i.e. slow cooking for 6 hours instead of 12), then you might have a problem. Because if you don't manage to kill all the bacteria, then the total required subsequent cooking time is going to creep back up as they multiply; that means your 6 hours in the slow cooker that might have been enough if you had seared the beef immediately before, are no longer enough to guarantee safe consumption.

So I am adding a caveat to my original answer: It is probably safe to refrigerate the browned beef, but you should calculate your cooking time as though you had never browned it. If you are concerned about safety (and I maintain the risks are minuscule), then treat the browned/refrigerated beef as uncooked meat. If you do that, I cannot see any reason why this wouldn't be safe.

You can cook Brisket to the point that it it is tender but sliceable, but that's tricky if you're slow cooking while at work or the like. Try topside, also often called salmon cut. It has a less a denser texture than brisket but still responds well to slow cooking.