The 90 days issue refers to changing IDs that are signed into a device. See and remove your devices that are associated with Apple ID purchases - View and remove your devices that are associated with Apple ID purchases - Apple Support - Read "More about associated devices" at the end where it refers to the 90 day wait. This applies to re-downloading past purchases (you can make new purchases), automatic downloads, and iCloud based services such as Family Sharing, Match, and Apple Music.
I am thinking what you want to do is use a primary ID but also have access to the items purchased with the secondary ID without having to swap between accounts all the time. Merging, splitting or transferring items between Apple accounts (IDs) is for the most part not officially supported. Read the links below for things you may need to do to transfer as much as is possible and to share some others.
Apps and media bought with one ID are permanently associated with that ID. Look into using Family Sharing to continue to be able to use items purchased with one Apple ID with other Apple IDs, and for some data sharing features.
- Family Sharing - What is Family Sharing? - Apple Support
- Set up Family Sharing - Set up Family Sharing - Apple Support
Share folders with iCloud Drive --> Share files and folders in iCloud Drive on iCloud.com - Apple Support
Read How to use Shared Albums in Photos on your iPhone, iPad, and Mac - Apple Support about how to share photos.
If you have signed into the first ID on a device then fortunately when you sign out of that ID, do not erase the device, then sign in with a different ID, it asks you in most cases if you wish to merge the data from the two IDs on your device (toggle the ones you want to on). Say yes and later delete individual items from the other ID that you do not want. Note, in How to save apps and progress on one Appl… - Apple Community a Community Specialist says, "you will not be able to transfer the meta data from one Apple ID to another. Once you switch to another Apple ID the information associated with the old Apple ID will be gone except for physical content on the device like photos and videos." Also turn off storage optimization before doing this. With Optimize Storage, smaller, space-saving photos and videos are kept on your device while all of your original, full-resolution versions are stored in iCloud. Make sure photo optimization is turned off. Manage your photo and video storage - Apple Support
Sign out of iCloud on your iPhone, iPad, iPod touch, Apple TV, or Mac --> Sign out of iCloud on your iPhone, iPad, iPod touch, Apple TV, or Mac - Apple Support
If another Apple ID is signed in you may need to enter the password for that ID to sign out of that ID first.
Click on this link to learn how to 'Sign in with your Apple ID' --> Sign in with your Apple ID - Apple Support
You will just stayed signed into your primary ID but have access to the apps via Family Sharing.
