Hello Whembegooz99
Only the Eurocity are always stopped at the border. The ICE are stopped only if they are late, sometimes in Basel Bad Bf (First stop, German station), sometimes in Basel SBB (Second stop, Swiss station).
It is no problem, you have other trains every 30 minutes from Basel to Wengen, simply take the next available ones, your ticket is still valid. Announcement are made in the train about the next connections, sometimes you can also take the tramway (line # 2) between the stations in Basel if no local train is available. Or follow the other passengers, you will not be alone.
You can also install the SBB Mobile app on your smartphone to search the next connections.
Kind regards
Danhiel