You should use the Notebook handling commands in MMA: The documentation is here
You have several options. You can open the notebooks programmatically and use the selection commands in the tutorial above to find and change text. Alternatively, you can do some string manipulation on the input cells of the notebooks. This is a sample of the second approach:
First get your files and set a new destination: (this example is on a Mac but its the same on a PC with different path specifications)
files = FileNames["/Users/xxx/Desktop/ToProcess/*.nb"]
newpath = "/Users/xxx/Desktop/Processed/"
Next, change the text in the files in bulk: (in this example, I changed ArcSin to ArcCos -- you can do whatever you want but realize the input cells were brought in and converted to strings by my code)
Map[Export[newpath<>FileNameTake[#],Notebook[StringReplace[NotebookImport[#,"Input"->"InputText"],"ArcSin"->"ArcCos"]]]&,files]
Now evaluate the new files in bulk:
filesToEval = FileNames[newpath <> "*.nb"]
evalNotebook[name_] :=
Module[{nb}, nb = NotebookOpen[name];
NotebookEvaluate[nb, InsertResults -> True];
NotebookSave[nb]; NotebookClose[nb]]
Map[evalNotebook, filesToEval]
Since you gave no example, I am assuming that you can do this with simple text manipulation. If not, you may have to explore some of the other ways to import the notebook cells. You can keep them as expressions and use replace rules and pattern matchings. You can also use the selection commands to find and change things. I hope this will get you started. Please let me know what approach you finally decide to use.
Regards
Neil