1. If this is a shortcut that's prompting the repair (and it usually is) IMO the safest way to disable this is to get Orca from the Windows SDK (install from Orca.msi), open your MSI file after you've built it, go to the Property table (the tables are on the left) and add a new row (right click on the right side list of properties) with the name DISABLEADVTSHORTCUTS (that's case-sensitive) and the value 1, then save the MSI file. You can't totally prevent repair because the user could right-click on your MSI file (opr use Add/Remove Programs) and force a repair, and there are other occasions when repair will kick in, but this should help.
2. The FAQ has this entry:
Q: How do I turn off repair for a file that I expect my users to modify?
A: There is a solution if you are willing to edit the .msi file after its
built.
For each file that you don't want automatically repaired, use ORCA or the
Windows Installer Automation to edit the Component table and delete the
Keypath entry. You'll need to use the File table to determine the Component
value for the rows to edit in the Component table.
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