If toss a used senko, or any other soft plastic, back in the bags with the fresh ones at the end of the day, will this affect the good ones in any way?  I

I do it and it doesn't seem to affect it.I use berkley so putting it back in the bag seems to put a little scent back on it.

However i have also been putting them back in a plano box prerigged for a quick pull out and retie on.

It dont hurt regular plastics but... If your talkin GYCB make sure the senko is dry or just put it in another bag. The moisture will add to the never ending problem of the baits becoming mushy as will excessive heat. Senkos are soft enough but when they get mushy they seem to fall right off the hook like butter.

Im sure most people know, but for those who dont. After you use a texas rig senko save it aside for wacky.