FontForge ignores second lookup flag when merging feature info file with multiple flags.
Example feature file:
lookup Kern_HEBR {
lookupflag RightToLeft IgnoreMarks;
pos \afii57645 \afii57681 -10;
pos \afii57645 \afii57664 -10;
} Kern_HEBR;
feature kern {
script hebr;
language dflt ;
lookup Kern_HEBR;
} kern;
After the import the lookup metadata shows just the first flag set:

The issue seems to be in fea_ParseLookupFlags()
FontForge ignores second lookup flag when merging feature info file with multiple flags.
Example feature file:
After the import the lookup metadata shows just the first flag set:

The issue seems to be in
fea_ParseLookupFlags()