I've only had success with e-ticket reissues by the issuing airline, there were always problems with what the other airline could see of the ticket. There is some procedure to pull the master of an e-ticket, but most agents are not familiar with it (as they would never do this for any other e-ticket except the OWE tickets -- most other e-tickets can only be changed by the issuing airline). It is a definite problem, but can be worked on by phone.

As for the original question of what routes require paper, there is no list and it changes all the time (sometimes irrationally). In general small secondary airports lack e-ticket retrieval capability. All OW airlines claim to have full e-ticket capability implemented. In the past I've run into absurdities like BA can issue e-ticket on BA codeshare of AY flight, but AY requires paper ticket for the AY code on the same flight. This seems to be slowly improving each month, with e-tickets everywhere. I would guess that South American regional flights are the most likely to require paper tickets.