To get the most accurate answer, I recommend calling Casting at 407-828-1000.
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Disney Store is considered a separate entity under the Disney Umbrella. If he were to transition to the College Program, he would technically have to "quit" the Disney Store before starting his CP, resetting what ever time he has accrued. And time spent while on the College Program does not count towards Union Seniority or years of service with the Company.
Also, as far as Parks and Resorts are concerned discounts increase only for those classified as Part-Time or Full-Time Cast Members after three years of service. Seasonal Cast Members are not eligible. And for those who are Seasonal and transfer to Full or Part Time, their "Clock" doesnt start until the transition is made, the time is not bridged.
Time is bridged for those who have worked for the Company in a Full or Part Time capacity for at least five years, leave voluntarily (not fired or laid off), and then come back. The time is bridged though after five years of consecutive service after rejoining the Company.