I've done this extensively and successfully, so let me advise two tools, especially if you are using Lightroom 2. Note that I haven't used the 'Publish to Flickr' service now available in Lightroom 3, I'm pretty sure it's worth investigating first.
This worked flawlessly for me. It allows you to synchronize metadata added to images stored on Flickr with the original versions of those images stored locally on your hard drive. If you don't have the original version on your hard drive, the application can download the missing pictures for you. The app can sync the metadata two-way on a picture-by-picture and metadata field-by-field basis.
Here is what you need to keep in mind though: do not use LR at the same time. Exit the app before syncing. Once you have synced your metadata/tags, you need to let LR know it should update its own keywords database with the new tags you imported withFlickrMetadataSynchr, otherwise they won't show up. You do not need to re-import your JPG files if you have them already in LR: just select the files then use "Metadata > Read Metadata from File(s)". WARNING: this will replace the metadata that was in your LR catalog for said files, so make sure you write any metadata back first.
Let me clarify this last warning: say you imported JPG files in LR, then added some keywords. These keywords are stored in the catalog, not in the JPG's EXIF section. Before syncing with FlickrMetadataSynchr, select your files and use "Metadata > Save Metadata to File(s)" to write the keywords back as tags. Exit LR, then use FlickrMetadataSynchr to merge the tags from Flickr with yours. Now use "Metadata > Read Metadata from File(s)", and you should have all your tags as keywords, both the ones you added in LR, and the ones you imported from Flickr.
In any case, I strongly suggest your run FlickrMetadataSynchr in "Simulate updating Metadata" mode first, to evaluate what is going to happen.
A second tool I've used extensively works the other way around.
This app displays your local folders and your flickr sets and can establish synchronization rules between them. You can manage all your photos locally and FlickrSync will keep them updated in flickr. For about 6 months I didn't have a clue about color management and was uploading my Flickr photos in AdobeRGB space. A big no no. I converted all my JPG photos back to sRGB and used FlickrSync to replace the old files with the new versions. This is definitely a case where you do not want to invalidate the old photo page, lose your tag or any of the links going to that photo. That tool did the job, updating the existing photo on Flickr with my new sRGB file.