The RF will still work. The remotes sends RF to a base unit and the Base has IR emitters plugged into it or an IR blaster that flashes all of the equipment.
An IR system will use an IR repeater which still needs the remote pointed at the IR receiver( usually located close to the TV/Display) problems with IR repeater systems is if the remote is blocked while sending commands..the command is lost. If that command is in a macro usually something wont power on or off or the TV misses an input change and now the client/end user is confused and begins the button pressing in anger and leads to a late night call or weekend call
There's no worse feeling than that millisecond you're sure you are going to die after leaning your chair back a little too far.
