@shankarananth you are missing in target argument in your replace command, otherwise it will apply to all the available fields.
| makeresults
| eval target="backed(up", someotherfield="backed(up"
| replace "backed(up" with "backed-up"
| table target someotherfield
So correct query is
| makeresults
| eval target="backed(up", someotherfield="backed(up"
| replace "backed(up" with "backed-up" in target
| table target someotherfield
Here is another option with replace() evaluation function
| makeresults
| eval target="backed(up", someotherfield="backed(up"
| eval target=replace(target,"(backed)\((up)","\1\2")
| table target
However, better approach would be to use SEDCMD during index-time as suggested by @mayurr98 and @somesoni2, so that data is indexed as expected, rather than using search time field corrections. As per your question you are looking for index time correction.
You should also check out the feasibility of correcting the logging by application in the first place if the logged text is not as expected. Even if you don't own the code or the app is third party, you can always notify them of such correction with miss-spelled/incorrect logging!
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