Sometimes it is best to explain by example. Can you post an example of a merged profile that needs the type of editing that you are concerned about?
There may already be a WikiTree Help file that explains post merge editing, but if not, here is what it might say about footnotes and sources:
After a merge, you may see something like this:
=== Birth ===
:: 1660<ref>ABC</ref>
=== Birth ===
:: 1660<ref>XYZ</ref>
This should be changed to:
=== Birth ===
:: 1660<ref>ABC</ref><ref>XYZ</ref>
If, instead, you see something like this:
=== Birth ===
:: 1661<ref>ABC</ref>
=== Birth ===
:: 1664<ref>XYZ</ref>
Change it to:
=== Birth ===
:: 1661<ref>ABC</ref>
:: 1664<ref>XYZ</ref>
The above example is an oversimplification. Many footnotes include an 'S#'.
Maybe a better example, after the above edits, you may see:
=== Birth ===
:: 1660<ref>[[#S1|S1]]: Page 521</ref><ref>[[#S2|S2]]: Page 123</ref>
This syntax automatically connects it the correct source, which is shown in the post merge file:
== Sources ==
<span id='S1'>S1</span>: ABC
== Sources ==
<span id='S2'>S2</span>: XYZ
The connection is maintained even if the post merge profile is a big mess. To clean up the profile, simply copy all this source information together into one section:
== Sources ==
* <span id='S1'>S1</span>: ABC
* <span id='S2'>S2</span>: XYZ
WikiTree does a good job at maintaining a different 'S#' for each source. I have never seen two different sources having the same 'S#'.
If a source is duplicated, with two different S-numbers, they can be combined by deleting the duplicate source and changing the S-number in all the appropriate footnotes. This is a real pain and not necessary, but it does make a cleaner profile.
You can also hide these S-numbers and make a better profile:
=== Birth ===
:: 1660<ref>[[#S1|ABC]]: Page 521</ref><ref>[[#S2|XYZ]]: Page 123</ref>
== Sources ==
* <span id='S1'></span>: ABC
* <span id='S2'></span>: XYZ
As a side note: Often, a profile will use the term "Source: " repeatedly throughout the profile. I use the Search-and-Replace of my text editor to remove all instances of the term "Source: ". AFAIK, this term is redundent and is never needed.