Simple answer: Yes, all will be good.
The detailed response from the IDG Internet Rechartering Program Manager:
If the YP information is entered during Internet Rechartering, at Submittal the person record will be updated with the YP completion. The data will sync through although this is not immediate.
Councils validate based on the physical receipt of the certificate from Training Manage. And the Council may also check on the entry.
Not stated (but implicit) is that some Councils must authorize alternative YP training methods in the instances where the online certification cannot be obtained. This is unusual but does occur.
Following is from the FAQ for Internet Rechartering.
What is the process for resolving an error with Youth Protection Training?
Youth Protection is required to be current for each adult leader as of the effective date of the new charter term. If YP is not current, then at Check Roster an error will occur that must be resolved. Update Unit Roster is used to find if an existing registrant has recently completed training. Errors are also resolved if the adult provided their YP completion certificate, Enter the course and date completed on the person record at Update Member Data. Keep a copy of the certificate to turn in to the Council with the unit renewal. If an adult is new, YP completion is entered as the record is created. If an adult was promoted without YP, enter the completion. Each volunteer adult leader is verified for YP being current on her or his record. To be considered as current, the Youth Protection Training Course (Y01) must have been completed on or AFTER February 1, 2018.