I guess that as long as the reservation is for the same train number everything will be fine. It is not your fault that the railway company changed the time of departure. Luck that you discovered that the train leaves earlier.
You can add trains manually in the app, if you want.
Search for the connection on the app and scroll down, you will find the option add it manually
That’s OK. No need to add a manual trip here. Never had any problems with conductors about mismatching times.
There are WORKs-for a very long time-along the main tracks east of Praha-and they are also rebuilding the local stanice just east of HN. Times are adapted every week or so-the app from IR itself is very often OUTofDate as it is not updated regurlarly. use bahn.de or also mujvlak.cz
You do not need to REServe seats on these trains-its optional.