I'll give an answer as it's been a while and no one has answered this.
Since I posted the question I have done some debugging and I'd like to post it as an answer as it may help others debugging Amiga 500 keyboards.
First, since the keyboard had a broken plunger for the left amiga key (in addition to the 2 enter keys not working).. I took the keyboard fully apart to replace the plunger, lightly cleaned the contact side of the membrane, and inspected the contacts and plungers for the enter keys. They all looked fine.
Put it back together, and found the keys still did not work.
Then I looked at the schematic found here: https://linuxjedi.co.uk/2023/08/31/amiga-1200-restoration/
and got a meter out and measured the voltage at the Y-row pins on the keyboard IC. I found that they had zero volts when no key pressed, and 5 volts on the respective pins when the enter keys were pressed.
This, wrongly, made me assume the key switches were ok, and the problem was either with the keyboard IC, or something on the motherboard.
While I waited for a replacement keyboard PCB to come in (Why not swap in a known working one?) I also swapped the 2 CIA chips as one of them is used for the keyboard, and found no change. I also removed those chips and Paula, and contact cleaned the sockets, just in case. No change.
Got the new keyboard PCB in, installed it, and ... no change.
Now that's a problem.. since its only those two keys, and the keyboard has a serial interface to the motherboard.. It would have to be a very odd fault for it to be a problem somewhere on the motherboard since all the other keys worked.
So the next thing I did, and I should have done this before ordering a new keyboard PCB, was I shorted the column and row pins on the keyboard IC for the return key... and it worked.
Ah, it's the switches after all! So somehow, though the voltage at the Y pins seem correct with the keys pressed, maybe the contact in the switch is not quite good enough for the IC to recognize the keypress.
Finally -- I took the keyboard apart again -removing the return and enter keys.. be carefull these keys are held on with wire clips.. took it apart, cleaned the membrane contacts for the two keys with a swab dipped in 90% isopropyl alcohol.. replaced the plungers. Put it all back together again.. now the return key works!.. enter still doesn't work, but I suppose two things.. a little more cleaning on the contacts, and try another plunger as I'm sure the plungers I bought were just scavenged from some other Amiga 500 keyboard, there's no guarantee they were all in working condition.
I'm going to declare success as I don't need the numeric keypad enter key, the main problem was the return key. Though the CLI will accept ctrl-m in the place of enter on a command line, other apps insist on the actual return key to be pressed. (for instance, to rename a folder in Workbench.. you have to press enter to finish, ctrl-m just puts a ctrl char in the name.
More info:
For the Amiga 500 keyboard, all the small keys are held on just friction fit into the plunger top. When you pull them off with a puller, be careful because there is a spring that will go flying.
For the wide keys, in order for them to press evenly they also have a wire clip that balances the press. Be extra careful pulling these off, as the eyelet end attached to the bottom of the keycap is friction fit into the keycap, and the wire is snapped into place on the keyboard top with 2 plastic hooks... if you are not careful you do risk breaking those hooks. so pull carefully up and away to one side. The return key is problematic since it has 2 wire clips at 90 degrees. in this case I pulled straight up carefully so that the eyelets came loose.
To put the return key back, what I found was it was best to unhook the wire clips from the keyboard and attach them to the keycap eyelets.. position the key with spring in place and carefully snap the wire under it's two plastic hooks. In order to do this with the return key I had to remove the shift key and the alt key below that, put the return key in first, then the shift, then the alt.
I may update the answer if I do decide to fix the enter key and it required a different approach.. I hope this answer serves as a guide to debug keyboards.