To add to Blacksheep's reply:
Repairs outside SRM limits accomplished by a Part 145 organisation - at least for EU registered aircraft involved in CAT (Commercial Air Transport) - must be designed and approved in accordance with EASA Part 21. As Blacksheep infers, this will usually be the TC holder but some minor repairs may be designed and approved by a "stand alone" Part 21 organisation.
As to whether the "patch" is replaced with a flush repair depends in some cases on lease return conditions and/or DTA (damage tolerance assessment) by the Part 21 organsiation.
Repairs should be mapped (I've reviewed such maps at Blacksheep's organisation; in fact it was part of his department).