Merging snapshots from 2 different builds does not give accurate code coverage result

We use DotCover during Hardening Sprint to capture code coverage on our QA environment. It is 2 week sprint during which we have to deploy newer builds on the QA environment so that we can regression test bugs which got fixed. While doing so, we get multiple snapshots, one per build. Once we merge these snapshots, we get incorrect code coverage data. Some lines which were shown as Covered in the previous build, are not shown covered after multiple build snapshot merge. Seems like a limitation DotCover has. If anyone has experienced this please respond to this post. If you could also comment on how you resolved that issue that would be great.
Thanks for your help in advance