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I think you are correct in smelling a rat.
does the car still start and run?
It may be possible that the code reader pulled up lots of faults but these maybe historic
when a fault occurs it stores the code and if undeleted it remains in the memory.
As the vehicle is running I can say that the cpu has not been fried it would not run if it was damaged to the extent they say.
I AM THINKING THAT THIS IS SOMETHING THEY HAVE CAUSED IN THE PROCESS OF CHANGING THE ALTERNATER.
The next step is for them to delete all stored fault codes run the engine and re scan .
If it is at all possible I would like to know what codes are remaining and can then offer more advice.
This is normal to display the engine check lamp and limited performance when the charging system is faulty as the control module will shut certain operating systems to conserve the important systems.
this question is open for another six days so I will await your report about the codes .