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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?
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words particle-か
Questions about phrase 「てもよいか」 and prefix 「うえ」
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
CC BY-SA 3.0
2016-10-14T03:41:56.470
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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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2016-10-14T04:28:27.013
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> 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?](https://japanese.stackexchange.com/q/13034/5010)

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](http://www.jgram.org/pages/viewOne.php?tagE=uede).

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.
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