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The Replacements dialog does not change the Alignment. If two lines are already aligned, the Replacements dialog lets you define a specific difference as equal/unimportant.
To change the Alignment, you would need to use the Session Settings, Alignment tab, and tweak settings here to see if they can be auto-aligned. Creating Line Weights in the Format may also have an impact on alignment.
I see, so you need Never Align Differences enabled. In that case, you must define a grammar for ".." and for "R:", and mark them as Unimportant. This will then align the lines as you expect.
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