Don't install an ini file as a file, but convert the entries into IniFile Table entries. This allows all ini file changes to be treated as "atomic change units" that allows proper merging and rollback via built-in MSI mechanism. You avoid all custom action complexity.
As Chris points out in his major upgrade comment: do things the right way in Wix / MSI and you avoid a lot of problems that start to pop up when requirements change or updates get complicated. IniFile updates implemented the right way are robust and simple to deal with.
In Wix you use the IniFile Element to achieve this. All merge capabilities, rollback support and advanced ini file handling comes along for free. All you need to do is to define what needs to be added or modified in the ini file during your installation. It will also be created if it is not there in the first place.
Using the IniFile element may look harder than it is. Here is a sample. You can also have a look at the well known Wix tutorial here.
All MSI-experts keep repeating this advice: never use a custom action to change a system if there are equivalent built-in MSI constructs.
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