I sent an email a Japanese former colleage of mine, and he replied several
weeks later. His reply included an emphatic apology for not replying sooner
(返信が遅くなってしまって本当にごめんなさい。） Is there a polite phrase I can use in my reply to
acknowledge his apology and let him know that I was not inconvenienced?

I am thinking 気にしないでください sounds inappropriately like forgiveness (when in fact
the delay was understandable and not a problem).
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2020-12-10T21:16:25.563
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politeness
In written correspondence, how do I politely say "it's OK" in response to an apology?
The apology might sound severe but this is just normal in written text. Don't
take it as the person being ashamed or anything.

Just a regular 「大丈夫です」or 「問題ないです」should suffice.
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"Not replying about it at all" is perhaps one of the valid options. It signals
"fine, let's just forget about it" without saying anything.

If you want to respond, just saying 気にしないでください or 大丈夫です might sound a little
blunt and unfriendly. It's best to explain why you were not bothered.
"まだ締め切りには時間がありますので気にしないでください", "特に急いでいないので全く問題ありません", etc.
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