In Rogue One, Jyn and Cassian break into the Imperial records vault while wearing uniforms they have taken from defeated imperial officers. This keeps them safe for a while, though ultimately they come under fire anyway. Jyn ends up on a catwalk, high over the planet's surface, targeted by a passing tie-fighter whose pilot presumably sees her rebel uniform. When and why did she take off her imperial uniform?
They "changed clothes" just before climbing through the broken glass to access the data stack they have to climb to get the data storage device since the mechanical arms don't do the job.
Since they have to climb the stack Jynn removes the restrictive 'armour-type thing she is wearing and the 'overalls' which are over her other clothes.
That's a lot of clothes to be wearing on a climb of that nature so it's natural she should, it's much easier to climb that way.
All Cassian does is remove his tunic/jacket and adds his gunbelt. He's still wearing the uniform trousers.
In any case, the fact there are rebels in the base is not a secret now. There's open gunfire both inside and outside the complex.