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I am able to create Two Way Replica from ArcGIS Server 10.4.1 which has a Feature service containing only one Feature Class( Transformers feature class) and I am getting a file like _ags_data{01D644C0D8F0434DA6E65607141EC0EC}.geodatabase in ArcGIS Server directory C:\arcgisserver\directories\arcgisoutput\Test_MapServer after creating the Replica.

Now I would like to check this file in an ArcMap session. I tried to connect to it through Database Connection tool but there is not any support for SQLLite on there. I also tried this link to Connect to SQLite from ArcGIS for Desktop but it says that the file must have the extension .sqlite (or .SQLITE or .SQLite) and not .geodatabase

Can you please let me know if there is a way to see the actual data in the _ags_data{01D644C0D8F0434DA6E65607141EC0EC}.geodatabase through ArcMap? I already tried to open the file by SQLLite Studio but the Feature class Transformers table in empty! so where are the actual attributes?

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The .geodatabase file you have is called a runtime geodatabase. In ArcMap 10.3.x and up, there's a tool called "copy-runtime-geodatabase-to-file-geodatabase", use that to convert it to a file Geodatabase and then open that in ArcMap.

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