Did some more testing and I think I see what's going on. When merging flight plans via the standard method the newly added aircraft are added to the list with the number they already had, as said. The newly added flight plans however are assigned the _first occurence of their previous acft number_ in the new list, so in most cases this an acft from the other file.
Example
Plan already open has, after previous modifications:
1 - Ce172
3 - B757
and I merge a plan to that with:
1 - DC-3
2 - F-4
3 - PA-28
The result is
1 - Ce172
3 - B757
1 - DC-3
2 - F-4
3 - PA-28
After that the DC-3 plans have the Ce172 (first #1), the F-4 plans are OK (first #2) and the PA-28 plans have the B757 (first #3).
And indeed, using Quick merge all is fine, as new acft numbers are added and used as expected!
Finally, 'Save as default search' sometimes does work for me in the new selection window. When it does, it is a perfect option, at least as fast and more flexible than via Windows. Most of the time however, I am presented with an empty list to go through from the start. Cannot put my finger on what causes this.
Erik