Hi Barry, I have added literally thousands of names to WikiTree using Gedcom files. So a little experience here.
I do not merge from a Gedcom file to an existing Profile unless that Profile is void of any sourced data or just has a Source like "From Personal Memory of So and So. That isn't a source, that's a memory. First of all, is your data markedly different than what is already there? If not, then mark it as Matched on your GEDCOMpare Report and move on. Why add what's already there and you'll just have to edit the Biography to remove duplicate information. You can Manually link any additional relatives you may add later. More on that below.
If so, manually add your data to the existing Profile. Merging data from a Gedcom file to an existing Profile can make a mess of that Profile and the clean up after wards is a real pain. Trust me on that from my experience...LOL I always check the Profile Manager's Page and their Contributions to see if they are Active on WikiTree (made a Contribution in the last 6 months is my rule) and contact them to let them know you have different additional data to add to that Profile. If the person you wish to add is a relative, that Profile Manager might a relative you didn't know about and you just made a real family connection. If the existing Profile is a Orphan, go ahead and add your data. Again,manually.
Regarding links, the Relationship Links are inherent in the Gedcom file and should not be lost. When you mark as Matched on the GEDCOMpare Report, GEDCOMpare will note this and additional linked names should stay linked. To make sure this is correct, add an immediate Family Member to WikiTree in the direct line of that person. Open another Tab on your browser and open that Profile and check to see if they are linked to the Existing Profile. If not, make the link then. You can stop adding names and verify linkage during the process before proceeding so you don't have to try and remember who is related to who.
On how links are created. The links in the present version of Gedcom files are lineal by a generation up or down the line. WikiTree follows that convention. Son or Daughter is linked to Father or Mother and their Children are Linked to them. Grandparents and Grandchildren are not directly linked in a Gedcom file to a name in said file. GEDCOMpare will not recognize a link to a Grandfather or Grandchildren when adding to WikiTree if adding them before the filial link was made on WikiTree. So that is a caveat to remember when adding names to WikiTree. Add names progressively through generational family lines or you can run into a Linked Names problem.