"I wonder if she will have to apply for Citizenship? And what will happen to her pension?"

She won't need to apply for citizenship Eliza. As I have aleady pointed out in the thread all British citizens habitually resident in Scotland will automatically qualify for Scottish citizenship! That has always been the stance of the SNP and it is stated in part 7 of the Scottish gvt's white paper on independence. Of course that is their proposal and they may not be the gvt in a future independent Scotland. However the idea that any of the other parties (Labour, Tories or Lib Dems) would seek to deny your sister citizenship is pretty far fetched.

The Scottish gvt has also published papers saying they will protect existing pension rights! Of course Musket is correct. As long as pensions can be afforded - but that applies to the UK itself as much as Scotland - however the Scottish gvt seems to be ringfencing pensions. Some argue that Scotland could possibly even afford to have improve pensions as just now according to some stats Scottish women get £11K less in their lifetime than women elsewhere in the UK and men £10K less. This though is due to lower life expectancy rates which I take it an independent Scottish gvt would seek to improve rather than use as a means to try and afford better pensions.