See the ?lavPredict help page for some details about different methods lavaan provides for estimate factor scores. The latest development version of lavaan suggests in the Examples section to use the plausibleValues() function, now available in the development version of semTools. To install both:
install.packages("lavaan", repos = "http://www.da.ugent.be", type = "source")
devtools::install_github("simsem/semTools/semTools")
To read about the plausible values approach, find references in this very brief Mplus report:
Estimating factor scores from the scalar invariance model should preserve the latent-mean differences you are interested in.
Are you referring to equating scales from different models? That is problematic because it assumes rather than tests the equivalence of all measurement parameters. I would recommend fitting all occasions in a single model, equating by literally imposing equality constraints on measurement parameters. If you are working with categorical indicators (you mentioned IRT), the semTools package also includes a syntax-writing function to facilitate sorting out all the identification vs. hypothesized-equality constrain issues: ?measEq.syntax
Terrence D. Jorgensen
Assistant Professor, Methods and Statistics
Research Institute for Child Development and Education, the University of Amsterdam