your belief is correct that we are going to lose localization and that simply by re-uploading the locales will solve the issue.
What we need as GitHub is a connection to a repo where Crowdin can take the source strings and then create an automatic branch for i18n where the translated ones are pushed as PRs.
We would need one for CP v1 and one for CP v2 I think since if I understand correctly they live in two different repos. Then I will be able to set the TMS (translation memories) that Crowdin uses to pretranslate correctly since the one for v1 goes with the v1 repo and the v2 with v2 repo.
Then Crowdin assumes that the repo where the software lives is the source (so that if new strings are added or strings are removed or changed only those changes get ported in Crowdin and all localizers get a notification that changes need to be translated/revised/approved, and the release that is generated pertains only to the changes made).
A notable thing to remember: Crowdin creates the PRs in a i18n repo, when you decide to merge translation into develop to do a release for CP you have to destroy that branch and Crowdin recreates it again when needed - that is necessary to avoid confusion.