I have seen other posts on this site with answers, but I think I have a slightly different scenario. My situation is as follows:
Some posts suggest this is a SVN 1.5 issue, but I'm sure I've upgraded the repos to 1.6+. How do I confirm this? And furthermore, how do I fix the tree conflict issue.
I'm using TortoiseSVN v1.6.8.
Read the SVN book. It boils down to this: When you create a branch, there can be two merge scenarios, 'catch-up' and 'reintegrate'. A catch-up merge is when you pull changes from the trunk into your branch. You can (and should) do this a lot, to make sure your branch doesn't diverge from the trunk too much. A reintegrate branch is what happens when you merge a branch back into the trunk. Because the way subversion tracks merges and changes, the branch is to be considered corrupt after this. If you need to continue working in that branch, the subversion book recommends you delete the branch right after the reintegrate merge and then re-create it from the merged trunk.