I am using Endnote X5 for my master thesis. Is there any way how I can
(1) format the bibliography to full justification without losing this format with every Endnote update in the document, and
(2) wrap the lines with a hyperlink in the bibliography so that the text is equally distributed in a line but that the hyperlink function remains (despite Endnote updates in the document)?
The paragraph information is dictated by the surrounding paragraphs at the end of the document (and this is probably dictated by the “normal” paragraph of your word document template, or an attribute you may have applied to the bibliography header). In word, if you “show” the paragraph symbols (those reverse Ps) select the whole of the bibliography and the following paragraph symbol, and apply justification, it should remain justified during updating. However, there is no way to get word (or endnote) to automatically break a hyperlink across a line, to make the justification look “normal”. You can do this as the last step before printing, after making a copy and unlinking the fields. If you then insert a space in the hyperlink, it will affect the displayed text (and let it break) but will not change the underlying hyperlink.
(the rest is totally off topic)
If you have a choice, readability statistics show that long documents are easier to read if they are not justified. That obviously doesn’t matter for the Bibliography, but if you can, your examiners will find a left aligned thesis easier to read (it is easier to track what line you are on) even if they don’t know why. Another trick is to always use a serif font rather than a non-serif font for long documents, if you have a choice. The brain can more easily distinguish the letters from one another. If these parameters are dictatated in your Universities instructions, you obviously can’t bypass them, but if they are not, consider making your examiners more relaxed while reading your thesis/dissertation!