They are actually stored on MSDB, you can verify it by below query
SELECT *
FROM msdb.dbo.sysssispackages
or you can call that package via SSDT/BIDS
1) Open the BDIS
2) Right click SSIS packages under the Solution Explorer
3) Select the option "Add Exisitng Package"
4) You will get a pop up asking the package location
5) Select SSIS Package Store for the first drop down
6) Enter your Server details
7) Click on the Button on the right hand side of the Package Path and this will list all the packages stored on that server both in the File system as well as the msdb. I feel in your case it ought to be in msdb
8) You can select and add it to your BDIS and make changes and reuse it again