You haven't mentioned what your average driving profile is. If as you say the garage told you it was too far gone ( A statement I find astonishing) then it would lead me to believe that your driving profile is not sufficient for the engine / ECU to initiate a regeneration. Perhaps too many short / urban journeys, which are detrimental to the optimal performance of a DPF equipped diesel engine, without the necessary low gear/ high speed cruise required to heat the engine sufficiently to trigger the regeneration correctly. The reason the lights would not go out and the DPF was not regenerating, was because the status of the engine i.e temperature, was not within the right parameters.
Because you made the choice to remove the DPF, in my opinion, there are only two options open to you for your current circumstances. One put the DPF back in and change your driving profile. Or two, approach the garage that did your remap and talk the problem through with them. I feel sure that this is where your problem lies
Perhaps you would probably be better off with a petrol engine.