A Mechanic reports lack of information in their Maintenance Tracking and Inventory computer system about previous aileron cable replacements contributed to numerous trouble shooting efforts to locate the cause of a clicking noise in a CRJ-200 control wheel.

Narrative

I am submitting this report due to just being made aware of an investigation in a CRJ-200 left aileron cable being misrouted at a Contract [Maintenance] Agency. I came on duty to find the CRJ-200 in work for a pilot squawk pertaining to clicking noise in the control wheel. The aircraft was in work and [Maintenance] had the directive to follow a certain [Bombardier] GREO (Generic Repair Engineering Order) for noise in control yoke. This GREO details the steps to follow to correct the discrepancy. The Maintenance Workcards drive you to follow the GREO. There was no binding reported in the discrepancy--only a clicking sound. When I arrived on the job-the GREO was already being complied with and retorque was accomplished. The GREO allows a retorque below the floor of the control column to correct the clicking sound.I did not personally feel the clicking or hear any unusual noises at all-so I directed our mechanics to assist me in the removal of the floor boards on the left side of the cabin to Detail Inspect the run of the cable from the control column to the cabin rear pressure floor area. The controls were being cycled back and forth for visual confirmation of any problems. There were no problems felt or seen under the floors. I had Inspection work with us and Visual (Visual Inspect) of the cables in the rear spar area of the wing and no defects were noted there.The wheel well area was inspected also and cable movement witnessed as satisfactory with no binding or clicking felt. This entire aircraft had been inspected deeply by several mechanics and inspectors to no avail. We then followed the GREO till completion; which stipulates that this is a one-time retorque and sets a fly-on for 500 hours; at which time the bearings must be replaced. That is what transpired and the bearings were replaced. Again the direction is to follow the GREO for compliance. After the bearing replacement the ailerons were again squawked and this is when Maintenance found the mis-route of the aileron cable in the wheel well area. We at Air Carrier X did not at any time disturb the connection of this cable in question. It has been revealed to me that our Contract Agency in ZZZ changed these cables during Heavy Maintenance. This is where the mis-route occurred I believe. Not knowing what Contact Maintenance does-and how deep put all of Air Carrier X at a definite disadvantage in finding the problem. I requested a Maintenance Check Flight to verify normal flight handling and the Check Flight was performed normally and released for service. GREO [Chapter] in reference is (Maintenance Manual) MM 27-11-031. All Maintenance Manual procedures that we were directed to were followed and accomplished.The Contract Agency must provide; without a shadow of doubt; a complete inspection of any critical system that is disturbed. Complete and absolute RII (Required Inspection Item) buy back. I truly feel that more surveillance is needed to assure safety. I also feel that Contract Maintenance work performed should be entered into our Maintenance and Inventory tracking system faster than it currently is being done. The reason for my thought is the aircraft is out of Heavy and has some problems and we mechanics do not know what system has been disturbed.