I checked reviews for the RiffStation software and the consensus seems to be that the chord detection ability is only useful for songs with very basic major or minor chords using the most common voicings with no inversions. In other words, more often than not, the chords it suggests are not all correct. So I would avoid using the program as a primary means of determining the chords to most songs.
But to your actual question
can I remove some short chords and use only 1 or 2 chord in the measures that I have more than 2? Does it hurt song quality?
The answer is - it depends.
If you are unable to play the actual full chords in the quick succession that are called for in a particular arrangement of a song, you can sometimes get away with omitting a passing chord - particularly if that passing chord is not a prominent feature of the song. Just because a particular chord would work with the underlying melody in a given measure, does not necessarily make it essential. If the chord you are holding (instead of playing the indicated transition chord) still works with the underlying melody - you can often skip the passing chord altogether.
Popular recorded versions of most songs have a certain sound, feel, and vibe that partially arises out of the chord progression used. Of course other elements such as rhythm, tempo, time signature, and the instruments used in the mix will also contribute to the unique signature of a given version of a given song.
As a musician who plays primarily for the fun of entertaining others - when I learn to cover another artist's song using the guitar as my accompaniment instrument, I attempt to replicate to the extent I am capable of (using the guitar) - a musical rendition that captures some semblance of the sound and feel and mood of the original. I want my cover to sound somewhat authentic and recognizable.
But there are songs that have fast moving chord changes that are difficult for me to pull off in real time - especially in front of a live audience. So what I often do in that situation, is simply substitute the root base note for a quick 2nd or 3rd chord in a measure, as I transition to the final chord of that measure. Played with proper timing and rhythm, this method often lends a surprising degree of authenticity to the passage.
Other songs might have fast changes that include chords that are difficult to transition between with the speed demanded by the song. Sometimes instead of using bass notes, I will use a substitute chord or alternate voicing of the chord used in the song. Or sometime a power chord (using two of the fatter strings) will make a good substitute for a full chord.
Ultimately you want to create a rendition that sounds recognizable and maintains most of the signature distinctive elements of the song that define that song. Without the full band using the same instruments with the same talent as the original band, no matter what you play - your are not going to sound like the original. So how you pull off the illusion is not as important as how the overall performance sounds to the audience.
If you can't play it exactly like the original artist or band - use whatever tricks, shortcuts, or substitutes make your performance sound as close as possible to the version you are attempting to emulate (in accordance with your ability). Don't allow an unrealistic demand for perfection keep you from playing the music you enjoy!