Sometimes Magento Connect Manager does not show update even if it is available.
Try to apply Uninstall option next to M2E Pro record in Magento Connect Manager. After that, install M2E Pro via Magento Marketplace.
The latest Module version, including your existing M2E Pro data, will be installed from Magento Marketplace. The future M2E Pro upgrades via Magento Marketplace should be performed according to these instructions.
No data can be lost during an upgrade process. However, please, always back up your system prior to any upgrade related activity.