"If your application to a guild has been rejected, you can not apply to this guild for the next 30 days. Note that all applications are saved for 30 days. Also an application will vanish, if the applicant has joined another guild in the meantime."
Source- Tibia's Manual
Your character will not appear if you try to submit another application, you need to wait 30 days. A good workaround for this would be for the guild to invite you instead of having you fill out an application. Once they invite you, you do not have to go through the application process on the website. I verified this after I denied an application, I was still able to invite the character and she successfully was invited and joined the guild. Another thing you can do is just re-apply with another character on your account.