Merging issues deleting all changes in current branch

Hello,

I am not an expert with Bazaar and am running into a merge issue. I have a working branch "MyWorkingBranch" that I am on currently. I have changes checked into this branch. Our company has a trunk branch that MyWorkingBranch is based on. I want to merge trunk into "MyWorkingBranch" so I ran this command:
bzr merge bzr://ourserver/trunk/ so that it would only merge any changes from trunk into my working branch but I am noticing that all my changes are being overwritten with what is in trunk, including any new files I added being deleted.
I have done a bzr revert for now but how do I merge trunk into my working branch without all my changes on my working branch being overwritten?

Thanks!