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This is probably more of a communication issue than an engineering issue(despite how awful the latter is). You should probably feel out management's perception of what's in this project. For example, they may be fully aware that the implementation is a WTF from Hell. If they're aware of that, and they just want you to crank out the old college try, then go with a simple solution: read the value, do a Split() on CRLF, run your array manipulations, and Join() by CRLF to update. Yeah, it has concurrency issues, but if there's only going to be one person using it, then resist the urge to over-engineer. Think of bigger problems, like world peace, hunger, third world debt, and what's going to happen on the next episode of "American Idol".
The other case may be that management is unaware of why the change they want would be difficult to do right. Do some explaining, make sure they're fully aware of the caveats, and ask for a judgement call. That's what they're there for - you're just supposed to make sure they get what they ask for and make sure they're clear on you not getting whipped for any poor risk decisions they make.