Mageflow Connector (MFX) can be upgraded in a number of ways. Each method depends on how you initially installed MFX. Methods of MFX Installation can be found in Installation Guide.
Steps to upgrade:
Go to Magento folder. Type:
modman update mfx
Go to Magento Connect Manager. Find Mageflow Connector extension from the list of installed extensions. Click “Upgrade” to upgrade to latest version.
Download the latest MFX version from Bitbucket Downloads. Extract the tgz package to a temporary folder. Copy the files with sFTP or rsync to your Magento folder while retaining the folder structure.