Depending on your scenario, this can be the result of a bug in CRM. If you have a BPF that has a conditional branch and you remove that branch then those records on a stage that was in a removed branch will be stuck. The only way I have found for fixing this is to use advanced find to query the BPF entity itself and delete the record from CRM...then you can refresh the record which had the BPF entity association and it will appear as no BPF is applied. From this point, you can use the "Process" button in the ribbon to set the active process.
If you're doing this for the Lead to Opportunity process, and you've Qualified the Lead already, then after you perform the same steps as above, you have to reopen the Lead, set the active process on that record, choose the next stage button and choose the already related opportunity, and then both will connect via the BPF flow. The problem is the Lead is still open and if you use the Qualify button then another Opportunity would get created or the BPF will error, so you can instead write a User On-demand workflow to Change the Lead Record status to Qualified.
