Yosemite Preview is not the same as Mavericks Preview!
Preview App in Yosemite renders annotations differently than Preview in Mavericks.
I have several PDFs that were annotated with previous versions of Preview that were great. Opening up those PDFs in Yosemite shows "stroked" text border around text boxes and a different font size, ruining the formatting and original annotation. It looks fine on Quicklook, but when the PDF is actually opened, there is change in the annotation formatting.
I have also tested opening these PDFs with Preview version 7 (from Mavericks) in Yosemite and everything appears as it always normally had. This definitely appears to be an issue with Version 8's rendering engine or layout engine. Note: I have only ever used Preview for these annotations
Here are some screenshots of the Preview issue:
First shot is of the PDF with Quicklook on Yosemite
Second shot is of the PDF opened with Preview 7 (Mavericks version) on Yosemite
Third shot is of the PDF opened with Preview 8 on Yosemite
OS X Yosemite (10.10), SL / Mavericks