Knowing what I do now, a soft spot in the roof would get the following treatment.
I would make small X cut where the roof is soft and work my way out from the center. I would make the X just big enough so that I could get to good lauan and then cut a hole making SURE I was out to good wood.
With the lauan cleaned up, it would also be critical that the main roof spars are in good shape. If you are repairing water damage, you will probably need to replace the insulation too.
Next, I would use some CPES (clear penetrating epoxy sealant) to seal the existing wood and cleanup the underside of rubber roof sheet too.
Once all the prep was done, I'd cut an appropriate sized roof patch from lauan, staple it back down and treat with CPES. If the seams could be felt, I would use wood putty to fill them and sand the whole patch area when the CPES dries. The sanding will make it possible to just use some 3M 90 contact cement to adhere the EPDM back down.
The last step would be to seal the X cut in the roof with some Eternabond and she would be good to go!
Jose