The conservation treatment of parchment can present many challenges. You can see in the document above that multiple seals are present, either made of paper and foil or wax and cloth. Care must be taken to preserve the seals, which behave somewhat independently from the vellum substrate. In this particular historical indenture, you can see evidence that the signature and several lines of text have been retouched at some point.
The likelihood is that the original signature had faded, and the owner wanted to improve the appearance. Unfortunately, the solvent they applied resulted in staining and bleeding of both the signature and the surrounding area, which left the yellow stain you now see. The signature was then redrawn, which you can determine by noting the much darker ink application in that area.
All in all, it goes to show that vellum and parchment are extremely sensitive materials. It takes skill, care and practice to handle them successfully, and the treatment of these materials is best entrusted to a conservator. If you require assistance with the care or restoration of your vellum document, feel free to submit an inquiry via the contact page on my website: http://mariannekelsey.com/contact-marianne-book-art-repair-restoration/