Of course, you could finish it and start the new one from top. But that's not very musical, isn't it? Why not connect the two hymns with the modulating interlude?
Here's one possible scenario:
1. Play the last line of Hymn #1 in the Tonic key on the main manual.
2. Play it in the relative key on the secondary manual.
3. Play the first line of the Hymn #2 in the relative key of the new hymn on the secondary manual. NOTE: If the keys in Steps 2 and 3 are not at all related, you may need to end the phrase of Step 2 with the Enharmonic modulation to the key of Step 3.
4. Play it in the Tonic key of this hymn but finish on the Dominant chord on the secondary manual.
5. Start Hymn #2 on the main manual.
Try it this Sunday at church and let me know how it went.