How to manage many databases with same schema in an easy way

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I have many databases (some of them big) of institutions (lets say hospitals), each one of them has his own encryption and all of them has the same schema.

Now if i try to merge them into a big one database, I have to manage the PK-FK problem (like in this: this post and this another, I tried to fix it manually doing the mapping of PKs and FKs using pragma and table info functions and schema table from sqlite (not compatible with all engines), but still I have to deal with ordering of insert commands because FK inserting before PK.

Now I want to know if there are a tool (ETL, Data Integration Tool, Data Fabric, etc), free or pay, to work with these many databases (all with same schema) and doing operation on them separately and hopefully making joins and unions of data.

So I have:

-hospital1.db

-hospital2.db

-hospital3.db

All with same schema and different encryption keys, I want any of these:

-Merge all the data (dealing with PK and FK mappings), beside the encryption method, all data without encryption.

-or using a tool or library to work with many of these databases separately and doing operations choosing which database to use, and hopefully making joins to analytical and other operations.

I have many of these, like n-databases (dozens and in the future some hundreds or thousand of these, from different organization and time)

Any advice will be greatfully apreciated too PD: forgive me about my grammar.

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