The current behaviour does not allow rolling upgrades, so remove the target version checks that disable the handler. In a future release develop a fix which allows rolling upgrades.
The FinalityHandler is disabled if the node doesn’t have any old apps installed (i.e. ones which don’t target version >= 4). If that node has a V4 app but a counterpart sends it a finalised transaction from a V3 app then the node with the V4 app won’t be able to receive the finalised transaction. The tx isn’t lost - the current thinking (well my thinking) was that the node operator would have to install the old app again and restart the node to recover the tx (the tx is never lost).