So i know that the mages guild dissolved into the synod and the college of whispers either during or just before it, but what about the othere. I know they are still around but did they break up during it and then come back together or did they just stay the same through it all?

The Fighter's Guild is presumably still around, since it's mentioned in a load screen. The Dark Brotherhood started breaking up around the 180s, and eventually all but disappears, but seems to have been fine during the interregnum. No idea about the thieve's guild.

Yes but im wondering if anything changed during interregnum, for example the fighters guild is practically an army, maybe whoever was master tried to use that to take the thrown or more likely many members left to go join certain armies, leaving it very small until the interregnum ended.

As far as I know, we don't know.