I wrote a script I included in AGAT called
agat_sp_prokka_fix_fragmented_gene_annotations.pl dedicated to detect fragmented genes due to frameshifts caused by small indels (1-2 nucleotide long) in PROKKA annotations. It allows to fix such cases by modifying your annotation and your fasta file when parameter activated.
I have heard the demand of such tool several times, so I hope it could help.
You can find some information here too.