Answer
Combine both conditions into a single $filter= expression joined with a lowercase and — for example, $filter=ProjectId eq $[PROJECT_ID] and SubProjectId eq $[SUB_PROJECT_ID] — rather than repeating the $filter= keyword for each condition or joining them with &, both of which only carry the last condition through to the target page. An uppercase AND has been reported to trigger a "malformed URL" server error, so the lowercase form is the one that's been confirmed to work.