There is no way around for the need to run “Update cross reference” but the following approach could avoid long running times at least for 1 environment. Please test that in a test environments first by also taking into consideration the following disclaimer:

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Prerequisite: You have 2 separate test environments with the same AX 2009 SP 1 (same kernel and application builds) versions available:

1) You install a new hotfix first in the test1 environment and check that it works and fits your needs

2) You run the time consuming “Update cross reference” job also in the test1 environment

3) Once step 2) succeeded you export the following tables from test1 environment xRefNames, xRefPaths, xRefReferences, xRefTableRelation, XRefTempReferences, and xRefTypeHierarchiery via Data Import/ Export functionality (Note: Tables starting with the name XRef* contain the result of the “Update cross reference” Run)

4) You install the hotfix in test2 environment

5) You import the following tables from test1 environment xRefNames, xRefPaths, xRefReferences, xRefTableRelation, XRefTempReferences, and xRefTypeHierarchiery via Data Import/ Export functionality into test2 environment