Once you have published or made changes in existing site workflow in Sharepoint Online site you will need to restart existing running workflow instances in order to get new changes into use (otherwise they won’t take effect). In order to restart existing site workflow instance in Sharepoint Online you may use the following steps. Go to Site settings > Site contents and click “Site workflows” link on the top of the page:
Opened page will show list of all available site workflows together with list of running workflows and list of completed workflows:
If you will click on some workflow name from the top list – it will be started. If you will click on some running workflow instance workflow details page will be opened:
On this page there is a link “End workflow” (it looks like regular text, not as a link). By clicking this link you may stop existing workflow instance, then return to previous page and start new instance which will use new published workflow version.