There are too many unknowns.
You did not indicate your travel dates. Train and bus and strike information are not available months ahead.
My recommendation would be :
1. When you are about 4 to 6 weeks before travel dates, google "Arles Girona bus". Or use Google Map's pubictransport function.
2. Consider the mainline factor
Bear in mind that Arles is - although wonderful and is one of my favorite cities - not on the train/bus mainline. All itineraries Arles-Girona will be long, involving 2 or more buses, sometimes with long waits in stations.
3. Consider Nîmes.
I read a post title by you where you express an interest in Romanesque architecture. Have you considered Nimes ? It is on the mainline and has more user-friendly buses to Girona. Nimes is bigger than Arles, has beautiful Roman ruins and other archeological gems, plus good food, especially at its market La Halle de Nîmes. If you make Nîmes your base, you can take a short train or local bus to arles. By local train it takes about 30 minutes. Longer by bus.