It would help to know if there was something specific that precipitated the change in the third week, but whether there was or not, things can still become better.
Unless it's necessary, I'd suggest that you not pick him up for a while so his discomfort isn't triggered.
I have a story to tell. Our approach was some different from the good advice above.
When we got our girls at almost 2 years old from their breeder, Noel was a happy, loved everybody little girl. Holly was scared of men, any man, even the breeders husband who I'm 100% sure never did anything to bring that on.
She didn't pee when picked up, she simply left any room that a man was in and would not let them in reach of her.
After we brought them home and we all settled in the first weeks, we didn't push the issue with her but we also knew that it would be necessary to at least get her to where my husband could touch her without her running away, if he needed to take her to the vet.
We started by having him be the one to feed them, so she'd associate that good thing with him. Another thing that we did was to sit on the sofa together for a short time with Holly in my lap. He would offer treats while we both encouraged her softly. If she took one, we'd both praise her and let her down. If she didn't, we still praise her and let her down or just sit quietly for a couple of minutes, then let her down. We did this several times a day.
Once she was taking treats pretty regularly and/or not trying to leave, I'd move her from my lap to between us and do the same thing.
Once that was going ok, I'd place her in his lap while still sitting right there and kept doing that until she didn't feel the need to leave.
Next we did this standing by each other, repeating the treats from him while Holly was in my arms. Since the middle step wasn't possible, once that was going ok, I'd hand her off to him, he'd hold her for a very brief time and then put her down.
We'd also leave a shirt or jacket with his scent near the places she liked to relax, to keep his scent near. Not in the bedtime crate, just in the daytime areas.
This went on for sometime, faster than a glacial pace, more like the changing of the seasons pace, with plateau time in between. We did push her just the tiniest bit past her comfort level, but only occasionally, with the hope that she'd see that nothing bad was going to happen.
We brought the girls home on October 4 2002 and it didn't take this long but the first picture I have of our success was August 13 2004. They were great together for the rest of her life.