Newer SonarQube versions do not have the 10K issues limitation.
You have to loop n-times to collect all results.
For example:
Consider a project with 44K issues.
You have to discover first how many issues you have to read, call one time the /api/issues/search with only you project key and the parameter ps ( pagesize ) equal to 100
http:///api/issues/search?componentKeys=&ps=100
You could receive an answer like this
{"total":44130,"p":1,"ps":100,"paging":{"pageIndex":1,"pageSize":100,"total":44130},"issues":[{"key":"AVtoCSNP6OwvnmtEJjae","ru..........
So we have to claim 44130 issues, using a pagesize of 100 then you must call (44130 / 100 ) + 1 times the /api/issues/search for your project and for every request remember to increase by 1 the p ( page ) parameter ( so you can point the right portion of results )
Your sequence of command will be like this
http:///api/issues/search?componentKeys=YOUR_PROJECT_KEY>&ps=100&p=1
http:///api/issues/search?componentKeys=YOUR_PROJECT_KEY>&ps=100&p=2
http:///api/issues/search?componentKeys=YOUR_PROJECT_KEY>&ps=100&p=3
....
http:///api/issues/search?componentKeys=YOUR_PROJECT_KEY>&ps=100&p=442
Parse the result of every call and you will be obtained the list of your issues.
Cheers
Massimo