2

The sentence came from Nintendo 3DS instruction manual explaining about transfer data from the earlier version, Nintendo DSi, to the newer one, Nintendo 3DS.

New 3DS本体にはDSiウェアのみ引っ越しされ、セーブデータは引っ越しされません。また、引っ越しすると、DSi本体では、ソフトと一緒にセーブデータも消去されます。引っ越しによってセーブデータを失ってもよいか、事前にご確認のうえ引っ越しを行ってください。

1) Does the 「か」in 「てもよいか」indicate doubt or uncertainty? In my opinion, since transferring the data to the new system, Nintendo 3DS, will cause the existing data in the original system, Nintendo DSi, being deleted for sure, I have a doubt why then the 「か」being written in the sentence.

2) If the prefix 「うえ」means before doing something, can I use 「前に」instead without losing the original meaning?

3

引っ越しによってセーブデータを失ってもよいか、事前にご確認のうえ引っ越しを行ってください。

This か is a question marker that introduces an embedded question. See this question: Usage of か after a clause?

So 「引っ越しによってセーブデータを失ってもよいか」 means "whether (or not) it's okay to lose your saved data by the move". を after the embedded question is usually omitted, as you can see in the link above.

verb + 上【うえ】 (+で) / noun + の上 (+で) is a formal set phrase that means "upon ~" or "after ~". You can see many examples here.

The sentence can be rephrased as:

引っ越しによってセーブデータを失ってもよいか(を)、確認した後で引っ越しを行ってください。
Perform the system transfer after you have confirmed you can lose your saved data.

2

In this case, the か indicates something that has to be confirmed(in form of a question). They are basically saying "confirm if 'is it acceptable to lose all your saved data'" and then, on top of doing that/after doing that(のうえ) proceed with the transfer.... or cancel if it is not an acceptable condition.

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1.According to "A Dictionary of Basic Japanese Grammar", page 168:
かどうか: a marker for an embedded yes-no question.

か is short for かどうか which means "whether".

Example:
鈴木さんが大学に入ったか知りません。
I don't know whether or not Mr. Suzuki entered college.

So in your case it becomes:
データを失ってもよいか、事前にご確認のうえ
Confirm beforehand whether the data may be lost or not.

2.If you want to replace うえ, you have to replace with 後に, not 前に

確認の後に
After confirming

確認の前に
Before confirming

  • You're missing the crucial part てもよいか: "confirm if it's OK to lose data". @stackreader has it right. – istrasci Oct 14 '16 at 4:58

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